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"type": "string", "description": "", "default": "-" } }, "required": [ "file1", "file2", "fields" ] } }, { "name": "csvtk_concat", "description": "Concatenate CSV/TSV files by rows.", "inputSchema": { "properties": { "files": { "type": "array", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "files" ] } }, { "name": "csvtk_uniq", "description": "Unique data without sorting.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "fields": { "type": "string", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "fields" ] } }, { "name": "csvtk_freq", "description": "Frequencies of selected fields.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "fields": { "type": "string", "description": "" }, "sort_by_freq": { "type": "boolean", "description": "", "default": false }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "fields" ] } }, { "name": "csvtk_mutate", "description": "Create new column from selected fields by regular expression.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "fields": { "type": "string", "description": "" }, "name": { "type": "string", "description": "" }, "pattern": { "type": "string", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "fields", "name", "pattern" ] } }, { "name": "csvtk_mutate2", "description": "Create a new column from selected fields by awk-like arithmetic/string expressions.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "name": { "type": "string", "description": "" }, "expression": { "type": "string", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "name", "expression" ] } }, { "name": "csvtk_rename", "description": "Rename column names with new names.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "fields": { "type": "string", "description": "" }, "names": { "type": "string", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "fields", "names" ] } }, { "name": "csvtk_replace", "description": "Replace data of selected fields by regular expression.", "inputSchema": { "properties": { "in_file": { "type": "string", "description": "" }, "fields": { "type": "string", "description": "" }, "pattern": { "type": "string", "description": "" }, "replacement": { "type": "string", "description": "" }, "tabs": { "type": "boolean", "description": "", "default": false }, "no_header_row": { "type": "boolean", "description": "", "default": false }, "out_file": { "type": "string", "description": "", "default": "-" } }, "required": [ "in_file", "fields", "pattern", "replacement" ] } }, { "name": "csvtk_round", "description": "Round float to n decimal places.", "inputSchema": { "properties": { 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"type": "boolean", "description": "", "default": false }, "restore": { "type": "boolean", "description": "", "default": false } }, "required": [] } }, { "name": "rscript_version", "description": "Retrieves the version of the Rscript interpreter and the R language.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_bioconductor-genomicalignments", "server_name": "bioconductor_genomicalignments", "path": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicalignments", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicalignments/app/bioconductor-genomicalignments_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicalignments/app/bioconductor-genomicalignments_server.py", "tool_count": 1, "tools": [ { "name": "summarize_overlaps", "description": "Generates a feature count matrix from alignment and annotation files.", 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"taxonomy_id": { "type": "number", "description": "", "default": null }, "chrominfo_file": { "type": "string", "description": "", "default": null }, "metadata_file": { "type": "string", "description": "", "default": null }, "pruning_mode": { "type": "string", "description": "", "default": "coarse" }, "on_foreign_chrom": { "type": "string", "description": "", "default": "abort" }, "infer_cds": { "type": "boolean", "description": "", "default": false }, "infer_utr": { "type": "boolean", "description": "", "default": true } }, "required": [ "gff_file", "output_db_path" ] } } ] }, { "server_dir": "mcp_bioconductor-genomicranges", "server_name": "bioconductor_genomicranges", "path": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicranges", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicranges/app/bioconductor-genomicranges_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-genomicranges/app/bioconductor-genomicranges_server.py", "tool_count": 11, "tools": [ { "name": "granges_reduce", "description": "Merge overlapping and adjacent genomic ranges into a single range.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "" }, "min_gapwidth": { "type": "number", "description": "", "default": 1 }, "ignore_strand": { "type": "boolean", "description": "", "default": false }, "with_revmap": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_file", "output_file" ] } }, { "name": "granges_intersect", "description": "Find the intersection of two sets of genomic ranges.", "inputSchema": { "properties": { "query_file": { "type": "string", "description": "" }, "subject_file": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "" }, "ignore_strand": { "type": "boolean", "description": "", "default": false } }, "required": [ "query_file", "subject_file", "output_file" ] } }, { "name": "granges_union", "description": "Find the union of two sets of genomic ranges.", "inputSchema": { "properties": { "query_file": { "type": "string", "description": "" }, "subject_file": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "" }, "ignore_strand": { "type": "boolean", "description": "", "default": false } }, "required": [ "query_file", "subject_file", "output_file" ] } }, { "name": "granges_setdiff", "description": "Find the set difference between two sets of genomic ranges (query - subject).", "inputSchema": { "properties": { "query_file": { "type": "string", "description": "" }, "subject_file": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "" }, "ignore_strand": { "type": "boolean", "description": "", "default": false } }, "required": [ "query_file", 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"" }, "pheno_data_file": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "pheno_data_sheet": { "type": "string", "description": "", "default": null }, "pheno_data_dcc_col_name": { "type": "string", "description": "", "default": "Sample_ID" }, "protocol_data_col_names": { "type": "array", "description": "", "default": null }, "experiment_data_col_names": { "type": "array", "description": "", "default": null } }, "required": [ "dcc_files_dir", "pkc_files", "pheno_data_file", "output_rds_path" ] } }, { "name": "set_segment_qc_flags", "description": "Sets segment QC flags in a NanoStringGeomxSet object based on specified cutoffs.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "min_segment_reads": { "type": "number", "description": "", "default": 1000 }, "percent_aligned": { "type": "number", "description": "", "default": 80 }, "percent_saturation": { "type": "number", "description": "", "default": 50 }, "min_negative_count": { "type": "number", "description": "", "default": 10 }, "max_ntc_count": { "type": "number", "description": "", "default": 1000 }, "min_nuclei": { "type": "number", "description": "", "default": 200 }, "min_area": { "type": "number", "description": "", "default": 16000 } }, "required": [ "input_rds_path", "output_rds_path" ] } }, { "name": "set_bioprobe_qc_flags", "description": "Sets probe QC flags in a NanoStringGeomxSet object.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "min_probe_ratio": { "type": "number", "description": "", "default": 0.1 }, "percent_fail_grubbs": { "type": "number", "description": "", "default": 20 }, "remove_local_outliers": { "type": "boolean", "description": "", "default": true } }, "required": [ "input_rds_path", "output_rds_path" ] } }, { "name": "subset_geomx_set", "description": "Subsets a NanoStringGeomxSet object based on phenotype (pData) or feature (fData) annotations.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "subset_by_pdata": { "type": "boolean", "description": "", "default": true }, "subset_column": { "type": "string", "description": "", "default": null }, "subset_values": { "type": "array", "description": "", "default": null } }, "required": [ "input_rds_path", "output_rds_path" ] } }, { "name": "aggregate_counts", "description": "Aggregates probe-level counts to the target level in a NanoStringGeomxSet object.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "elt": { "type": "string", "description": "", "default": "exprs" } }, "required": [ "input_rds_path", "output_rds_path" ] } }, { "name": "normalize_geomx", "description": "Normalizes the count data in a NanoStringGeomxSet object.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_rds_path": { "type": "string", "description": "" }, "norm_method": { "type": "string", "description": "" }, "from_elt": { "type": "string", "description": "", "default": "exprs" }, "to_elt": { "type": "string", "description": "", "default": "exprs_norm" }, "housekeepers": { "type": "array", "description": "", "default": null } }, "required": [ "input_rds_path", "output_rds_path", "norm_method" ] } }, { "name": "mixed_model_de", "description": "Performs differential expression analysis using a linear mixed model.", "inputSchema": { "properties": { "input_rds_path": { "type": "string", "description": "" }, "output_csv_path": { "type": "string", "description": "" }, "elt": { "type": "string", "description": "" }, "model_formula_fixed": { "type": "string", "description": "" }, "group_var": { "type": "string", "description": "" }, "model_formula_random": { "type": "string", "description": "", "default": null }, "contrasts": { "type": "array", "description": "", "default": null }, "n_cores": { "type": "number", "description": "", "default": 1 } }, "required": [ "input_rds_path", "output_csv_path", "elt", "model_formula_fixed", "group_var" ] } } ] }, { "server_dir": "mcp_bioconductor-ggsc", "server_name": "bioconductor_ggsc", "path": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-ggsc", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-ggsc/app/bioconductor-ggsc_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-ggsc/app/bioconductor-ggsc_server.py", "tool_count": 4, "tools": [ { "name": "plot_reduced_dim", "description": "Generates a reduced dimension plot (e.g., UMAP, t-SNE) from a SingleCellExperiment object.", "inputSchema": { "properties": { "input_rds": { "type": "string", "description": "" }, "output_plot": { "type": "string", "description": "" }, "dim_red": { "type": "string", "description": "" }, "color_by": { "type": "string", "description": "" }, "facet_by": { "type": "string", "description": "", "default": null }, "plot_title": { "type": "string", "description": "", "default": null }, "img_width": { "type": "number", "description": "", "default": 7 }, "img_height": { "type": "number", "description": "", "default": 7 } }, "required": [ "input_rds", "output_plot", "dim_red", "color_by" ] } }, { "name": "plot_gene_expression", "description": "Plots the expression of a single gene on a reduced dimension plot.", "inputSchema": { "properties": { "input_rds": { "type": "string", "description": "" }, "output_plot": { "type": "string", "description": "" }, "gene": { "type": "string", "description": "" }, "dim_red": { "type": "string", "description": "" }, "assay": { "type": "string", "description": "", "default": "logcounts" }, "plot_title": { "type": "string", "description": "", "default": null }, "img_width": { "type": "number", "description": "", "default": 7 }, "img_height": { "type": "number", "description": "", "default": 7 } }, "required": [ "input_rds", "output_plot", "gene", "dim_red" ] } }, { "name": "plot_expression_heatmap", "description": "Generates a heatmap of gene expression for a set of genes.", "inputSchema": { "properties": { "input_rds": { "type": "string", "description": "" }, "output_plot": { "type": "string", "description": "" }, "genes": { "type": "array", "description": "" }, "annotation_col": { "type": "string", "description": "" }, "assay": { "type": "string", "description": "", "default": "logcounts" }, "plot_title": { "type": "string", "description": "", "default": null }, "img_width": { "type": "number", "description": "", "default": 7 }, "img_height": { "type": "number", "description": "", "default": 10 } }, "required": [ "input_rds", "output_plot", "genes", "annotation_col" ] } }, { "name": "plot_expression_violin", "description": "Generates a violin plot of gene expression across different groups.", "inputSchema": { "properties": { "input_rds": { "type": "string", "description": "" }, "output_plot": { "type": "string", "description": "" }, "gene": { "type": "string", "description": "" }, "group_by": { "type": "string", "description": "" }, "assay": { "type": "string", "description": "", "default": "logcounts" }, "plot_title": { "type": "string", "description": "", "default": null }, "img_width": { "type": "number", "description": "", "default": 7 }, "img_height": { "type": "number", "description": "", "default": 5 } }, "required": [ "input_rds", "output_plot", "gene", "group_by" ] } } ] }, { "server_dir": "mcp_bioconductor-ggspavis", "server_name": "bioconductor_ggspavis", "path": "/225040511/project/Biomni/mcp_generated/mcp_bioconductor-ggspavis", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"default": false }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 }, "pplacer_path": { "type": "string", "description": "", "default": null }, "hmmer_path": { "type": "string", "description": "", "default": null }, "prodigal_path": { "type": "string", "description": "", "default": null } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "tree", "description": "Constructs a phylogenetic tree from a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": 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"", "default": 1 } }, "required": [ "marker_gene_folder", "genome_folder", "output_folder" ] } }, { "name": "plot", "description": "Generates various plots for visualizing genome quality.", "inputSchema": { "properties": { "checkm_output_folder": { "type": "string", "description": "" }, "image_folder": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "image_file": { "type": "string", "description": "", "default": null }, "image_type": { "type": "string", "description": "", "default": "png" }, "font_size": { "type": "number", "description": "", "default": 12 }, "dpi": { "type": "number", "description": "", "default": 300 }, "width": { "type": "number", "description": "", "default": 10.0 }, "height": { "type": "number", "description": "", "default": 8.0 }, "title": { "type": "string", "description": "", "default": null }, "label": { "type": "string", "description": "", "default": null }, "color": { "type": "string", "description": "", "default": null }, "marker_size": { "type": "number", "description": "", "default": 10 }, "line_width": { "type": "number", "description": "", "default": 1 }, "force": { "type": "boolean", "description": "", "default": false }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false } }, "required": [ "checkm_output_folder", "image_folder" ] } }, { "name": "ssu_finder", "description": "Identifies SSU rRNA genes in genome files.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "unique_markers", "description": "Identifies unique marker genes for a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "profile", "description": "Profiles the distribution of marker genes across a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "tetra", "description": "Calculates tetranucleotide frequencies for a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "dist", "description": "Calculates genomic characteristics distributions for a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "coverage", "description": "Calculates coverage statistics for a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "tab_output_file": { "type": "string", "description": "", "default": null }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "force": { "type": "boolean", "description": "", "default": false }, "tmpdir": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "len_hist", "description": "Generates a length histogram for a set of genomes.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_folder": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "image_file": { "type": "string", "description": "", "default": null }, "image_type": { "type": "string", "description": "", "default": "png" }, "font_size": { "type": "number", "description": "", "default": 12 }, "dpi": { "type": "number", "description": "", "default": 300 }, "width": { "type": "number", "description": "", "default": 10.0 }, "height": { "type": "number", "description": "", "default": 8.0 }, "title": { "type": "string", "description": "", "default": null }, "label": { "type": "string", "description": "", "default": null }, "color": { "type": "string", "description": "", "default": null }, "force": { "type": "boolean", "description": "", "default": false }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "nx_plot", "description": "Generates an 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"default": false }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false } }, "required": [ "genome_folder", "output_folder" ] } }, { "name": "bin_set", "description": "Creates a set of bins from a folder of genome files.", "inputSchema": { "properties": { "genome_folder": { "type": "string", "description": "" }, "output_bin_set_file": { "type": "string", "description": "" }, "extension": { "type": "string", "description": "", "default": "fna" }, "output_file": { "type": "string", "description": "", "default": null }, "force": { "type": "boolean", "description": "", "default": false }, "quiet": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false } }, "required": [ "genome_folder", "output_bin_set_file" ] } } ] }, { "server_dir": "mcp_circexplorer2", "server_name": "circexplorer2", "path": 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"description": "", "default": false }, "threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "library_file", "fastq_files", "sample_labels", "output_prefix" ] } }, { "name": "mageck_test", "description": "Run the MAGeCK 'test' command to perform statistical tests on a count table.", "inputSchema": { "properties": { "count_table": { "type": "string", "description": "" }, "treatment_samples": { "type": "array", "description": "" }, "control_samples": { "type": "array", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "sgrna_len": { "type": "number", "description": "", "default": 20 }, "adjust_method": { "type": "string", "description": "", "default": "fdr" }, "sort_by": { "type": "string", "description": "", "default": "pos" }, "variance_estimation_samples": { "type": "array", "description": "", "default": null }, "remove_zero": { "type": "string", "description": "", "default": "none" }, "remove_zero_threshold": { "type": "number", "description": "", "default": 0 }, "norm_method": { "type": "string", "description": "", "default": "median" }, "control_sgrna": { "type": "string", "description": "", "default": null }, "paired": { "type": "boolean", "description": "", "default": false }, "permutation_round": { "type": "number", "description": "", "default": 10000 }, "pdf_plot": { "type": "boolean", "description": "", "default": false }, "gene_lfc_method": { "type": "string", "description": "", "default": "alphamean" }, "gene_test_fdr_threshold": { "type": "number", "description": "", "default": 0.25 }, "cnv_norm": { "type": "string", "description": "", "default": null }, "cell_line": { "type": "string", "description": "", "default": null }, "control_gene": { "type": "string", "description": "", "default": null } }, "required": [ "count_table", "treatment_samples", "control_samples", "output_prefix" ] } }, { "name": "mageck_mle", "description": "Run the MAGeCK 'mle' command for Maximum-Likelihood Estimation based analysis.", "inputSchema": { "properties": { "count_table": { "type": "string", "description": "" }, "design_matrix": { "type": "string", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "sgrna_len": { "type": "number", "description": "", "default": 20 }, "norm_method": { "type": "string", "description": "", "default": "median" }, "control_sgrna": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 }, "permutation_round": { "type": "number", "description": "", "default": 10000 }, "pdf_plot": { "type": "boolean", "description": "", "default": false }, "gene_lfc_method": { "type": "string", "description": "", "default": "alphamean" }, "gene_test_fdr_threshold": { "type": "number", "description": "", "default": 0.25 }, "cnv_norm": { "type": "string", "description": "", "default": null }, "cell_line": { "type": "string", "description": "", "default": null }, "control_gene": { "type": "string", "description": "", "default": null }, "beta_labels": { "type": "array", "description": "", "default": null } }, "required": [ "count_table", "design_matrix", "output_prefix" ] } }, { "name": "mageck_pathway", "description": "Run the MAGeCK 'pathway' command for pathway enrichment analysis.", "inputSchema": { "properties": { "gene_ranking": { "type": "string", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "gmt_file": { "type": "string", "description": "", "default": null }, "permutation": { "type": "number", "description": "", "default": 1000 }, "fdr_method": { "type": "string", "description": "", "default": "fdr" }, "pathway_size_min": { "type": "number", "description": "", "default": 10 }, "pathway_size_max": { "type": "number", "description": "", "default": 500 } }, "required": [ "gene_ranking", "output_prefix" ] } }, { "name": "mageck_flute", "description": "Run the MAGeCK 'flute' command for visualizing MAGeCK results.", "inputSchema": { "properties": { "gene_summary": { "type": "string", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "treatment_id": { "type": "array", "description": "", "default": null }, "control_id": { "type": "array", "description": "", "default": null }, "top": { "type": "number", "description": "", "default": 5 }, "remove_prefix": { "type": "boolean", "description": "", "default": false }, "x_axis": { "type": "string", "description": "", "default": null }, "y_axis": { "type": "string", "description": "", "default": null }, "label_column": { "type": "string", "description": "", "default": null }, "width": { "type": "number", "description": "", "default": 8.0 }, "height": { "type": "number", "description": "", "default": 6.0 }, "plot_type": { "type": "string", "description": "", "default": "volcano" }, "scale_by_size": { "type": "boolean", "description": "", "default": false }, "day0": { "type": "boolean", "description": "", "default": false } }, "required": [ "gene_summary", "output_prefix" ] } }, { "name": "mageck_vispr", "description": "Run the MAGeCK 'vispr' command to generate files for VISPR visualization.", "inputSchema": { "properties": { "count_table": { "type": "string", "description": "" }, "sample_labels": { "type": "array", "description": "" }, "design_matrix": { "type": "string", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "sgrna_len": { "type": "number", "description": "", "default": 20 }, "norm_method": { "type": "string", "description": "", "default": "median" }, "project_name": { "type": "string", "description": "", "default": null } }, "required": [ "count_table", "sample_labels", "design_matrix", "output_prefix" ] } } ] }, { "server_dir": "mcp_mameshiba", "server_name": "mameshiba", "path": "/225040511/project/Biomni/mcp_generated/mcp_mameshiba", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_mameshiba/app/mameshiba_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_mameshiba/app/mameshiba_server.py", "tool_count": 2, "tools": [ { "name": "mameshiba", "description": "Runs MameShiba, a lightweight version of Shiba, for splicing analysis.", "inputSchema": { "properties": { "config_yaml": { "type": "string", "description": "" }, "processes": { "type": "number", "description": "", "default": 4 } }, "required": [ "config_yaml" ] } }, { "name": "scshiba", "description": "Runs scShiba to quantify and identify differential splicing events from single-cell RNA-seq data.", "inputSchema": { "properties": { "config_yaml": { "type": "string", "description": "" }, "processes": { "type": "number", "description": "", "default": 4 } }, "required": [ "config_yaml" ] } } ] }, { "server_dir": "mcp_mappy", "server_name": "mappy", "path": "/225040511/project/Biomni/mcp_generated/mcp_mappy", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_mappy/app/mappy_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_mappy/app/mappy_server.py", "tool_count": 2, "tools": [ { "name": "minimap2_index", "description": "Creates a minimap2 index (.mmi) from a reference FASTA/FASTQ file.", "inputSchema": { "properties": { "reference_file": { "type": "string", "description": "" }, "output_index_file": { "type": "string", "description": "" }, "kmer_size": { "type": "number", "description": "", "default": null }, "window_size": { "type": "number", "description": "", "default": null }, "homopolymer_compressed": { "type": "boolean", "description": "", "default": false }, "batch_size": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 3 } }, "required": [ "reference_file", "output_index_file" ] } }, { "name": "minimap2_align", "description": "Performs sequence alignment using minimap2.", "inputSchema": { "properties": { "reference_input": { "type": "string", "description": "" }, "query_files": { "type": "array", "description": "" }, "output_file": { "type": "string", "description": "" }, "output_format": { "type": "string", "description": "", "default": "paf" }, "preset": { "type": "array", "description": "", "default": null }, "output_cigar_paf": { "type": "boolean", "description": "", "default": false }, "num_secondary_alignments": { "type": "number", "description": "", "default": 5 }, "secondary_ratio": { "type": "number", "description": "", "default": 0.8 }, "long_cigar_tag": { "type": "boolean", "description": "", "default": false }, "cs_tag": { "type": "string", "description": "", "default": null }, "force_strand": { "type": "string", "description": "", "default": null }, "splice_flank_no": { "type": "boolean", "description": "", "default": false }, "junction_bed_file": { "type": "string", "description": "", "default": null }, "junction_bonus": { "type": "number", "description": "", "default": 9 }, "max_intron_length": { "type": "number", "description": "", "default": 200000 }, "write_junctions_file": { "type": "string", "description": "", "default": null }, "pass1_junctions_file": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 3 } }, "required": [ "reference_input", "query_files", "output_file" ] } } ] }, { "server_dir": "mcp_markerrepo", "server_name": "markerrepo", "path": "/225040511/project/Biomni/mcp_generated/mcp_markerrepo", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_markerrepo/app/markerrepo_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_markerrepo/app/markerrepo_server.py", "tool_count": 4, "tools": [ { "name": "markerrepo_clone", "description": "Clones a marker repository from a given git URL to a specified local path.", "inputSchema": { "properties": { "url": { "type": "string", "description": "" }, "path": { "type": "string", "description": "" } }, "required": [ "url", "path" ] } }, { "name": "markerrepo_update", "description": "Updates a local marker repository by pulling the latest changes from the remote.", "inputSchema": { "properties": { "path": { "type": "string", "description": "" } }, "required": [ "path" ] } }, { "name": "markerrepo_list", "description": "Lists available markers in a local repository, with optional filtering.", "inputSchema": { "properties": { "repo_path": { "type": "string", "description": "" }, "species": { "type": "string", "description": "", "default": null }, "tissue": { "type": "string", "description": "", "default": null } }, "required": [ "repo_path" ] } }, { "name": "markerrepo_annotate", "description": "Annotates a scanpy AnnData object (.h5ad) using markers from a repository.", "inputSchema": { "properties": { "repo_path": { "type": "string", "description": "" }, "adata_path": { "type": "string", "description": "" }, "output_path": { "type": "string", "description": "" }, "groupby": { "type": "string", "description": "", "default": "leiden" }, "species": { "type": "string", "description": "", "default": "human" }, "tissue": { "type": "string", "description": "", "default": null }, "key_added": { "type": "string", "description": "", "default": "cell_type" } }, "required": [ "repo_path", "adata_path", "output_path" ] } } ] }, { "server_dir": "mcp_mash", "server_name": "mash", "path": "/225040511/project/Biomni/mcp_generated/mcp_mash", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_mash/app/mash_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_mash/app/mash_server.py", "tool_count": 8, "tools": [ { "name": "mash_sketch", "description": "Create sketches (reduced representations for fast operations) from sequence files.", "inputSchema": { "properties": { "files": { "type": "array", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "kmer_size": { "type": "number", "description": "", "default": 21 }, "sketch_size": { "type": "number", "description": "", "default": 1000 }, "threads": { "type": "number", "description": "", "default": 1 }, "file_list": { "type": "string", "description": "", "default": null }, "individual_sequences": { "type": "boolean", "description": "", "default": false }, "reads": { "type": "boolean", "description": "", "default": false }, "min_copies": { "type": "number", "description": "", "default": 1 }, "min_coverage": { "type": "number", "description": "", "default": 1 }, "genome_size": { "type": "number", "description": "", "default": null }, "warning_threshold": { "type": "number", "description": "", "default": 0.01 }, "buffer_size": { "type": "string", "description": "", "default": null }, "verbose": { "type": "boolean", "description": "", "default": false }, "seed": { "type": "number", "description": "", "default": 42 }, "non_canonical": { "type": "boolean", "description": "", "default": false }, "amino_acid": { "type": "boolean", "description": "", "default": false }, "amino_acid_01": { "type": "boolean", "description": "", "default": false }, "comment": { "type": "string", "description": "", "default": null }, "concatenated": { "type": "boolean", "description": "", "default": false } }, "required": [ "files" ] } }, { "name": "mash_dist", "description": "Estimate the distance of query sequences to references.", "inputSchema": { "properties": { "reference_sketch": { "type": "string", "description": "" }, "query_files": { "type": "array", "description": "" }, "query_list": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 }, "tabular": { "type": "boolean", "description": "", "default": false }, "max_distance": { "type": "number", "description": "", "default": 1.0 }, "max_p_value": { "type": "number", "description": "", "default": 1.0 }, "sketch_size": { "type": "number", "description": "", "default": null }, "kmer_size": { "type": "number", "description": "", "default": null }, "seed": { "type": "number", "description": "", "default": 42 }, "top_pair_only": { "type": "boolean", "description": "", "default": false }, "amino_acid": { "type": "boolean", "description": "", "default": false }, "amino_acid_01": { "type": "boolean", "description": "", "default": false }, "individual_sequences": { "type": "boolean", "description": "", "default": false }, "write_comments": { "type": "string", "description": "", "default": null }, "read_comments": { "type": "string", "description": "", "default": null } }, "required": [ "reference_sketch", "query_files" ] } }, { "name": "mash_screen", "description": "Determine whether query sequences are within a larger mixture of sequences.", "inputSchema": { "properties": { "reference_sketch": { "type": "string", "description": "" }, "query_files": { "type": "array", "description": "" }, "threads": { "type": "number", "description": "", "default": 1 }, "p_value_threshold": { "type": "number", "description": "", "default": 0.01 }, "winner_takes_all": { "type": "boolean", "description": "", "default": false }, "identity_threshold": { "type": "number", "description": "", "default": 0.95 }, "bloom_filter_size": { "type": "string", "description": "", "default": null }, "no_bloom_filter": { "type": "boolean", "description": "", "default": false }, "amino_acid": { "type": "boolean", "description": "", "default": false }, "amino_acid_01": { "type": "boolean", "description": "", "default": false }, "seed": { "type": "number", "description": "", "default": 42 } }, "required": [ "reference_sketch", "query_files" ] } }, { "name": "mash_triangle", "description": "Estimate a lower-triangular distance matrix from a single sketch file.", "inputSchema": { "properties": { "sketches": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 }, "list_names_only": { "type": "boolean", "description": "", "default": false }, "omit_query_vs_query": { "type": "boolean", "description": "", "default": false }, "max_distance": { "type": "number", "description": "", "default": 1.0 }, "max_p_value": { "type": "number", "description": "", "default": 1.0 }, "write_comments": { "type": "string", "description": "", "default": null }, "read_comments": { "type": "string", "description": "", "default": null } }, "required": [ "sketches" ] } }, { "name": "mash_paste", "description": "Create a single sketch file from multiple sketch files.", "inputSchema": { "properties": { "output_name": { "type": "string", "description": "" }, "sketch_files": { "type": "array", "description": "" }, "sketch_list_file": { "type": "string", "description": "", "default": null } }, "required": [ "output_name", "sketch_files" ] } }, { "name": "mash_info", "description": "Display information about sketch files.", "inputSchema": { "properties": { "sketch_files": { "type": "array", "description": "" }, "tabular": { "type": "boolean", "description": "", "default": false }, "show_comments": { "type": "boolean", "description": "", "default": false }, "show_data": { "type": "boolean", "description": "", "default": false } }, "required": [ "sketch_files" ] } }, { "name": "mash_bounds", "description": "Print a table of Mash error bounds. This command takes no arguments.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "mash_taxscreen", "description": "Create a Kraken-style taxonomic report based on mash screen output.", "inputSchema": { "properties": { "taxonomy_map": { "type": "string", "description": "" }, "screen_output": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "threads": { "type": "number", "description": "", "default": 1 }, "taxonomy_tree": { "type": "string", "description": "", "default": null }, "taxonomy_names": { "type": "string", "description": "", "default": null }, "min_identity": { "type": "number", "description": "", "default": 0.95 }, "min_hashes": { "type": "number", "description": "", "default": 10 }, "rank": { "type": "string", "description": "", "default": "species" }, "report_unclassified": { "type": "boolean", "description": "", "default": false }, "report_zeroes": { "type": "boolean", "description": "", "default": false } }, "required": [ "taxonomy_map", "screen_output" ] } } ] }, { "server_dir": "mcp_maxquant", "server_name": "maxquant", "path": "/225040511/project/Biomni/mcp_generated/mcp_maxquant", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_maxquant/app/maxquant_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_maxquant/app/maxquant_server.py", "tool_count": 3, "tools": [ { "name": "maxquant_run", "description": "Runs the MaxQuant analysis pipeline using a specified mqpar.xml configuration file.", "inputSchema": { "properties": { "mqpar_xml_file": { "type": "string", "description": "" }, "maxquant_cmd_path": { "type": "string", "description": "" }, "num_threads": { "type": "number", "description": "", "default": null } }, "required": [ "mqpar_xml_file", "maxquant_cmd_path" ] } }, { "name": "maxquant_create_mqpar", "description": "Creates a template MaxQuant parameter file (mqpar.xml) from FASTA files.", "inputSchema": { "properties": { "output_xml_path": { "type": "string", "description": "" }, "fasta_files": { "type": "array", "description": "" }, "maxquant_cmd_path": { "type": "string", "description": "" } }, "required": [ "output_xml_path", "fasta_files", "maxquant_cmd_path" ] } }, { "name": "maxquant_change_folder", "description": "Updates all file paths in a mqpar.xml file to point to a new data folder.", "inputSchema": { "properties": { "mqpar_xml_file": { "type": "string", "description": "" }, "new_data_folder": { "type": "string", "description": "" }, "maxquant_cmd_path": { "type": "string", "description": "" }, "output_xml_path": { "type": "string", "description": "", "default": null } }, "required": [ "mqpar_xml_file", "new_data_folder", "maxquant_cmd_path" ] } } ] }, { "server_dir": "mcp_medaka", "server_name": "medaka", "path": "/225040511/project/Biomni/mcp_generated/mcp_medaka", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_medaka/app/medaka_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_medaka/app/medaka_server.py", "tool_count": 7, "tools": [ { "name": "medaka_consensus", "description": "Creates consensus sequences and variant calls from nanopore sequencing data using neural networks.", "inputSchema": { "properties": { "input_basecalls": { "type": "string", "description": "" }, "draft_assembly": { "type": "string", "description": "" }, "output_directory": { "type": "string", "description": "" }, "threads": { "type": "number", "description": "", "default": 1 }, "batch_size": { "type": "number", "description": "", "default": null }, "use_bacterial_model": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_basecalls", "draft_assembly", "output_directory" ] } }, { "name": "medaka_variant", "description": "Performs haploid variant calling from nanopore sequencing data.", "inputSchema": { 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"inputSchema": { "properties": { "x_values": { "type": "number", "description": "" }, "y_values": { "type": "number", "description": "" }, "yp1": { "type": "number", "description": "", "default": 1e+30 }, "ypn": { "type": "number", "description": "", "default": 1e+30 } }, "required": [ "x_values", "y_values" ] } }, { "name": "math_derivative_from_file", "description": "Reads numeric data from a file and calculates the 1st or 2nd order derivatives.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "order": { "type": "number", "description": "", "default": 1 }, "column_x": { "type": "number", "description": "", "default": 0 }, "column_y": { "type": "number", "description": "", "default": 1 }, "has_header": { "type": "boolean", "description": "", "default": false }, "yp1": { "type": "number", "description": "", "default": 1e+30 }, "ypn": { "type": "number", "description": "", "default": 1e+30 } }, "required": [ "input_file" ] } } ] }, { 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{ "numbers": { "type": "number", "description": "" }, "method": { "type": "string", "description": "", "default": "round" }, "multiple": { "type": "number", "description": "", "default": null } }, "required": [ "numbers" ] } } ] }, { "server_dir": "mcp_perl-math-spline", "server_name": "perl_math_spline", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-math-spline", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-math-spline/app/perl-math-spline_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-math-spline/app/perl-math-spline_server.py", "tool_count": 1, "tools": [ { "name": "math_spline_interpolate", "description": "Performs cubic spline interpolation using the Perl Math::Spline library.", "inputSchema": { "properties": { "input_data": { "type": "string", "description": "" }, "query_points": { "type": "string", "description": "" }, "output_file": { "type": "string", 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"description": "", "default": null }, "mode": { "type": "string", "description": "", "default": "positive" }, "precursor_mz": { "type": "number", "description": "", "default": null }, "precursor_adduct": { "type": "string", "description": "", "default": null }, "fragment_tol": { "type": "number", "description": "", "default": 0.01 }, "fragment_tol_unit": { "type": "string", "description": "", "default": "Da" }, "min_intensity": { "type": "number", "description": "", "default": 1.0 }, "max_depth": { "type": "number", "description": "", "default": 2 }, "verbose": { "type": "boolean", "description": "", "default": false } }, "required": [ "in_file", "out_file" ] } } ] }, { "server_dir": "mcp_perl-mime-lite", "server_name": "perl_mime_lite", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-mime-lite", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-mime-lite/app/perl-mime-lite_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-mime-lite/app/perl-mime-lite_server.py", "tool_count": 5, "tools": [ { "name": "mime_lite_send_email", "description": "Send an email with optional attachments using Perl's MIME::Lite.", "inputSchema": { "properties": { "sender": { "type": "string", "description": "" }, "recipient": { "type": "string", "description": "" }, "subject": { "type": "string", "description": "" }, "body": { "type": "string", "description": "" }, "content_type": { "type": "string", "description": "", "default": "text/plain" }, "cc": { "type": "string", "description": "", "default": "" }, "bcc": { "type": "string", "description": "", "default": "" }, "attachments": { "type": "array", "description": "", "default": null }, "send_method": { "type": "string", "description": "", "default": "sendmail" }, "smtp_server": { "type": "string", "description": "", "default": "localhost" } }, "required": [ "sender", "recipient", "subject", "body" ] } }, { "name": 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"include_dirs": { "type": "array", "description": "", "default": null } }, "required": [] } }, { "name": "perl_module_build_help", "description": "Returns the help documentation for Module::Build actions.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_perl-module-corelist", "server_name": "perl_module_corelist", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-corelist", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-module-corelist/app/perl-module-corelist_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-corelist/app/perl-module-corelist_server.py", "tool_count": 8, "tools": [ { "name": "query_module", "description": "Finds in which version(s) of perl a given module was shipped in the core distribution.", "inputSchema": { "properties": { "module_name": { "type": "string", "description": "" }, "list_all_versions": { "type": "boolean", "description": "", "default": false } }, "required": [ "module_name" ] } }, { "name": "query_perl_version", "description": "Lists all modules or only deprecated modules shipped with a specific version of perl.", "inputSchema": { "properties": { "perl_version": { "type": "string", "description": "" }, "list_deprecated": { "type": "boolean", "description": "", "default": false } }, "required": [ "perl_version" ] } }, { "name": "compare_perl_versions", "description": "Shows the differences in modules between two perl versions.", "inputSchema": { "properties": { "perl_version1": { "type": "string", "description": "" }, "perl_version2": { "type": "string", "description": "" }, "output_format": { "type": "string", "description": "", "default": "text" }, "diff_type": { "type": "string", "description": "", "default": "modules" } }, "required": [ "perl_version1", "perl_version2" ] } }, { "name": "list_perl_versions", "description": "Lists all perl versions for which Module::CoreList has data.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "list_all_modules", "description": "Lists all modules for which Module::CoreList has data.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "list_all_deprecated_modules", "description": "Lists all deprecated modules for which Module::CoreList has data.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "query_feature", "description": "Shows in which perl version a given feature (e.g., 'say') appeared.", "inputSchema": { "properties": { "feature_name": { "type": "string", "description": "" } }, "required": [ "feature_name" ] } }, { "name": "get_version", "description": "Shows the version of the Module::CoreList data.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_perl-module-load-conditional", "server_name": "perl_module_load_conditional", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-load-conditional", "command": [ 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"boolean", "description": "", "default": false } }, "required": [ "module_name" ] } }, { "name": "can_load_modules", "description": "Determines if a list of Perl modules can be loaded, and loads them if all are possible.", "inputSchema": { "properties": { "modules": { "type": "string", "description": "" }, "verbose": { "type": "boolean", "description": "", "default": false }, "nocache": { "type": "boolean", "description": "", "default": false }, "autoload": { "type": "boolean", "description": "", "default": false }, "check_inc_hash": { "type": "boolean", "description": "", "default": false }, "force_safe_inc": { "type": "boolean", "description": "", "default": false }, "clear_cache": { "type": "boolean", "description": "", "default": false } }, "required": [ "modules" ] } }, { "name": "get_module_requirements", "description": "Retrieves a list of other modules that a particular Perl module requires.", "inputSchema": { "properties": { "module_name": { "type": "string", "description": "" }, "check_inc_hash": { "type": "boolean", "description": "", "default": false }, "force_safe_inc": { "type": "boolean", "description": "", "default": false } }, "required": [ "module_name" ] } } ] }, { "server_dir": "mcp_perl-module-metadata", "server_name": "perl_module_metadata", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-metadata", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-module-metadata/app/perl-module-metadata_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-metadata/app/perl-module-metadata_server.py", "tool_count": 11, "tools": [ { "name": "determine_packages", "description": "Determines packages from given Perl module files. Corresponds to the --determine-packages flag.", "inputSchema": { "properties": { "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "files" ] } }, { "name": "get_package_version", "description": "Determines the version of a given package from Perl module files. Corresponds to the --package-version flag.", "inputSchema": { "properties": { "package": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "package", "files" ] } }, { "name": "get_module_version", "description": "Determines the version of a given module from Perl module files. Corresponds to the --module-version flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_requires", "description": "Determines the requirements of a given module. Corresponds to the --requires flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_optional_requires", "description": "Determines the optional requirements of a given module. Corresponds to the --optional-requires flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_recommends", "description": "Determines the recommended requirements of a given module. Corresponds to the --recommends flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_suggests", "description": "Determines the suggested requirements of a given module. Corresponds to the --suggests flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_conflicts", "description": "Determines the conflicting requirements of a given module. Corresponds to the --conflicts flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_build_requires", "description": "Determines the build requirements of a given module. Corresponds to the --build-requires flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_configure_requires", "description": "Determines the configure requirements of a given module. Corresponds to the --configure-requires flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } }, { "name": "get_module_test_requires", "description": "Determines the test requirements of a given module. Corresponds to the --test-requires flag.", "inputSchema": { "properties": { "module": { "type": "string", "description": "" }, "files": { "type": "array", "description": "" }, "no_index": { "type": "boolean", "description": "", "default": false }, "inc": { "type": "array", "description": "", "default": null } }, "required": [ "module", "files" ] } } ] }, { "server_dir": "mcp_perl-module-runtime", "server_name": "perl_module_runtime", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime/app/perl-module-runtime_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime/app/perl-module-runtime_server.py", "tool_count": 1, "tools": [ { "name": "perl_module_runtime_info", "description": "This function serves as a placeholder to address the request for 'perl-module-runtime'.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_perl-module-runtime-conflicts", "server_name": "perl_module_runtime_conflicts", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime-conflicts", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime-conflicts/app/perl-module-runtime-conflicts_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-module-runtime-conflicts/app/perl-module-runtime-conflicts_server.py", "tool_count": 1, "tools": [ { "name": "check_module_runtime_conflicts", "description": "Checks for version conflicts related to the Perl module Module::Runtime.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_perl-moo", "server_name": "perl_moo", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-moo", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"type": "string", "description": "", "default": null }, "debugging_flags": { "type": "string", "description": "", "default": null }, "no_sitecustomize": { "type": "boolean", "description": "", "default": false }, "split_pattern": { "type": "string", "description": "", "default": null }, "edit_in_place_extension": { "type": "string", "description": "", "default": null }, "include_directories": { "type": "array", "description": "", "default": null }, "line_ending_processing": { "type": "string", "description": "", "default": null }, "modules_to_use": { "type": "array", "description": "", "default": null }, "loop_around_program": { "type": "boolean", "description": "", "default": false }, "loop_and_print": { "type": "boolean", "description": "", "default": false }, "rudimentary_switch_parsing": { "type": "boolean", "description": "", "default": false }, "search_path_for_programfile": { "type": "boolean", "description": "", "default": false }, "tainting_warnings": { "type": "boolean", "description": "", "default": false }, "tainting_checks": { "type": "boolean", "description": "", "default": false }, "dump_core_after_parsing": { "type": "boolean", "description": "", "default": false }, "allow_unsafe_operations": { "type": "boolean", "description": "", "default": false }, "print_version": { "type": "boolean", "description": "", "default": false }, "print_config_summary": { "type": "string", "description": "", "default": null }, "enable_warnings": { "type": "boolean", "description": "", "default": false }, "enable_all_warnings": { "type": "boolean", "description": "", "default": false }, "ignore_text_before_perl_line": { "type": "string", "description": "", "default": null }, "disable_all_warnings": { "type": "boolean", "description": "", "default": false } }, "required": [] } } ] }, { "server_dir": "mcp_perl-moose", "server_name": "perl_moose", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-moose", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-moose/app/perl-moose_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-moose/app/perl-moose_server.py", "tool_count": 1, "tools": [ { "name": "perl_interpreter", "description": "Executes a script using the Perl interpreter.", "inputSchema": { "properties": { "programfile": { "type": "string", "description": "", "default": null }, "arguments": { "type": "array", "description": "", "default": null }, "execute_program": { "type": "array", "description": "", "default": null }, "execute_program_extended": { "type": "array", "description": "", "default": null }, "record_separator": { "type": "string", "description": "", "default": null }, "autosplit": { "type": "boolean", "description": "", "default": false }, "unicode_features": { "type": "string", "description": "", "default": null }, "check_syntax_only": { "type": "boolean", "description": "", "default": false }, "debugger": { "type": "string", "description": "", "default": null }, "debugging_flags": { "type": "string", "description": "", "default": null }, "no_sitecustomize": { "type": "boolean", "description": "", "default": false }, "split_pattern": { "type": "string", "description": "", "default": null }, "in_place_edit": { "type": "string", "description": "", "default": null }, "include_dirs": { "type": "array", "description": "", "default": null }, "line_ending_processing": { "type": "string", "description": "", "default": null }, "modules": { "type": "array", "description": "", "default": null }, "loop_around_program": { "type": "boolean", "description": "", "default": false }, "loop_and_print": { "type": "boolean", "description": "", "default": false }, "enable_switch_parsing": { "type": "boolean", "description": "", "default": false }, "search_path_for_program": { "type": "boolean", "description": "", "default": false }, "taint_warnings": { "type": "boolean", "description": "", "default": false }, "taint_checks": { "type": "boolean", "description": "", "default": false }, "dump_core": { "type": "boolean", "description": "", "default": false }, "allow_unsafe": { "type": "boolean", "description": "", "default": false }, "print_version": { "type": "boolean", "description": "", "default": false }, "print_config": { "type": "string", "description": "", "default": null }, "enable_warnings": { "type": "boolean", "description": "", "default": false }, "enable_all_warnings": { "type": "boolean", "description": "", "default": false }, "extract_from_text": { "type": "string", "description": "", "default": null }, "disable_all_warnings": { "type": "boolean", "description": "", "default": false } }, "required": [] } } ] }, { "server_dir": "mcp_perl-net-http", "server_name": "perl_net_http", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-net-http", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-net-http/app/perl-net-http_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-net-http/app/perl-net-http_server.py", "tool_count": 5, "tools": [ { "name": "net_http_request", "description": "Performs a low-level HTTP request using the Net::HTTP Perl module.", "inputSchema": { "properties": { "host": { "type": "string", "description": "" }, "method": { "type": "string", "description": "", "default": "GET" }, "uri": { "type": "string", "description": "", "default": "/" }, "port": { "type": "number", "description": "", "default": 80 }, "headers": { "type": "array", "description": "", "default": null }, "content": { "type": "string", "description": "", "default": "" }, "keep_alive": { "type": "boolean", "description": "", "default": false }, "send_te": { "type": "boolean", "description": "", "default": false }, "http_version": { "type": "string", "description": "", "default": "1.1" }, "max_line_length": { "type": "number", "description": "", "default": 8192 }, "max_header_lines": { "type": "number", "description": "", "default": 128 }, "laxed": { "type": "boolean", "description": "", "default": false } }, "required": [ "host" ] } }, { "name": "net_http_format_request", "description": "Formats an HTTP request message and returns it as a string without sending it.", "inputSchema": { "properties": { "host": { "type": "string", "description": "" }, "method": { "type": "string", "description": "", "default": "GET" }, "uri": { "type": "string", "description": "", "default": "/" }, "headers": { "type": "array", "description": "", "default": null }, "content": { "type": "string", "description": "", "default": "" }, "keep_alive": { "type": "boolean", "description": "", "default": false }, "http_version": { "type": "string", "description": "", "default": "1.1" } }, "required": [ "host" ] } }, { "name": "net_http_format_chunk", "description": "Returns the string to be written for a given chunk of data in a chunked transfer.", "inputSchema": { "properties": { "data": { "type": "string", "description": "" } }, "required": [ "data" ] } }, { "name": "net_http_format_chunk_eof", "description": "Returns the string to be written for signaling EOF when a Transfer-Encoding of chunked is used.", "inputSchema": { "properties": { "trailers": { "type": "array", "description": "", "default": null } }, "required": [] } }, { "name": "net_http_get_config", "description": "Returns the configuration summary of the installed Perl environment and Net::HTTP version.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_perl-net-ssleay", "server_name": "perl_net_ssleay", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-net-ssleay", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-net-ssleay/app/perl-net-ssleay_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-net-ssleay/app/perl-net-ssleay_server.py", "tool_count": 2, "tools": [ { "name": "ssleay_version", "description": "Retrieves version and build information for the OpenSSL library used by Net::SSLeay.", "inputSchema": { "properties": { "all_info": { "type": "boolean", "description": "", "default": false }, "build_info": { "type": "boolean", "description": "", "default": false }, "compiler_info": { "type": "boolean", "description": "", "default": false }, "dir_info": { "type": "boolean", "description": "", "default": false }, "engines": { "type": "boolean", "description": "", "default": false }, "features": { "type": "boolean", "description": "", "default": false }, "openssl_version": { "type": "boolean", "description": "", "default": false }, "platform": { "type": "boolean", "description": "", "default": false }, "seeding": { "type": "boolean", "description": "", "default": false }, "build_targets": { "type": "boolean", "description": "", "default": false }, "script_version": { "type": "boolean", "description": "", "default": false } }, "required": [] } }, { "name": "sslecho", "description": "A simple SSL/TLS echo client for testing server connections.", "inputSchema": { "properties": { "host_port": { "type": "string", "description": "" }, "cert_file": { "type": "string", "description": "", "default": null }, "key_file": { "type": "string", "description": "", "default": null }, "ca_path": { "type": "string", "description": "", "default": null }, "ca_file": { "type": "string", "description": "", "default": null }, "verify_level": { "type": "number", "description": "", "default": null }, "verbose": { "type": "boolean", "description": "", "default": false }, "debug": { "type": "boolean", "description": "", "default": false }, "ssl_protocol": { "type": "string", "description": "", "default": null } }, "required": [ "host_port" ] } } ] }, { "server_dir": "mcp_perl-number-format", "server_name": "perl_number_format", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-number-format", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-number-format/app/perl-number-format_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_perl-number-format/app/perl-number-format_server.py", "tool_count": 7, "tools": [ { "name": "format_number", "description": "Formats a number with a specific precision and grouping separators (commas).", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "precision": { "type": "number", "description": "", "default": 2 }, "trailing_zeros": { "type": "boolean", "description": "", "default": true } }, "required": [ "number" ] } }, { "name": "format_negative", "description": "Formats a negative number according to a specified format (picture).", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "picture": { "type": "string", "description": "", "default": "(-)" } }, "required": [ "number" ] } }, { "name": "format_currency", "description": "Formats a number as a currency string.", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "symbol": { "type": "string", "description": "", "default": "$" }, "precision": { "type": "number", "description": "", "default": 2 } }, "required": [ "number" ] } }, { "name": "format_bytes", "description": "Formats a number of bytes into a human-readable string (K, M, G, etc.).", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "precision": { "type": "number", "description": "", "default": 2 } }, "required": [ "number" ] } }, { "name": "format_percentage", "description": "Formats a number as a percentage string.", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "precision": { "type": "number", "description": "", "default": 2 } }, "required": [ "number" ] } }, { "name": "unformat_number", "description": "Converts a formatted string back into a raw numeric value.", "inputSchema": { "properties": { "formatted_string": { "type": "string", "description": "" } }, "required": [ "formatted_string" ] } }, { "name": "format_price", "description": "A specialized version of format_number often used for prices, ensuring", "inputSchema": { "properties": { "number": { "type": "number", "description": "" }, "precision": { "type": "number", "description": "", "default": 2 } }, "required": [ "number" ] } } ] }, { "server_dir": "mcp_perl-ole-storage_lite", "server_name": "perl_ole_storage_lite", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-ole-storage_lite", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_perl-ole-storage_lite/app/perl-ole-storage_lite_shim_server.py" ], "metadata_source": 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"type": "boolean", "description": "", "default": false }, "dump_core": { "type": "boolean", "description": "", "default": false }, "allow_unsafe_operations": { "type": "boolean", "description": "", "default": false }, "print_version": { "type": "boolean", "description": "", "default": false }, "print_config_summary": { "type": "string", "description": "", "default": null }, "enable_warnings": { "type": "boolean", "description": "", "default": false }, "enable_all_warnings": { "type": "boolean", "description": "", "default": false }, "ignore_text_before_perl_line": { "type": "string", "description": "", "default": null }, "disable_all_warnings": { "type": "boolean", "description": "", "default": false } }, "required": [] } } ] }, { "server_dir": "mcp_perl-package-deprecationmanager", "server_name": "perl_package_deprecationmanager", "path": "/225040511/project/Biomni/mcp_generated/mcp_perl-package-deprecationmanager", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"single_end": { "type": "boolean", "description": "", "default": false }, "compress": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_file", "out_prefix" ] } }, { "name": "rseqc_bam2wig", "description": "Convert BAM file into wig/bigWig format. BAM must be sorted and indexed.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "chrom_size": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "wigsum": { "type": "number", "description": "", "default": null }, "skip_multi_hits": { "type": "boolean", "description": "", "default": false }, "strand": { "type": "string", "description": "", "default": "none" }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file", "chrom_size", "out_prefix" ] } }, { "name": "rseqc_bam_stat", "description": "Summarizing mapping statistics of a BAM or SAM file.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file" ] } }, { "name": "rseqc_clipping_profile", "description": "Calculate the distributions of clipped nucleotides across reads.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "mapq": { "type": "number", "description": "", "default": 30 }, "sequencing": { "type": "string", "description": "", "default": "SE" } }, "required": [ "input_file", "out_prefix" ] } }, { "name": "rseqc_deletion_profile", "description": "Calculate the distributions of deletions across reads.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "read_align_length": { "type": "number", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "read_num": { "type": "number", "description": "", "default": 1000000 }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_bam", "read_align_length", "out_prefix" ] } }, { "name": "rseqc_divide_bam", "description": "Equally divide BAM file into n parts.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "subset_num": { "type": "number", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "skip_unmap": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_file", "subset_num", "out_prefix" ] } }, { "name": "rseqc_fpkm_count", "description": "Calculate raw read count, FPM and FPKM for each gene in BED file.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "strand": { "type": "string", "description": "", "default": "none" }, "skip_multi_hits": { "type": "boolean", "description": "", "default": false }, "only_exonic": { "type": "boolean", "description": "", "default": false }, "mapq": { "type": "number", "description": "", "default": 30 }, "single_read": { "type": "number", "description": "", "default": 1.0 } }, "required": [ "input_file", "refgene_bed", "out_prefix" ] } }, { "name": "rseqc_fpkm_uq", "description": "Calculate count, FPKM, and FPKM-UQ values defined by TCGA. Requires HTSeq.", "inputSchema": { "properties": { "bam_file": { "type": "string", "description": "" }, "gtf_file": { "type": "string", "description": "" }, "info_file": { "type": "string", "description": "" }, "output_prefix": { "type": "string", "description": "" }, "log2": { "type": "boolean", "description": "", "default": false } }, "required": [ "bam_file", "gtf_file", "info_file", "output_prefix" ] } }, { "name": "rseqc_genebody_coverage", "description": "Calculate the RNA-seq reads coverage over gene body.", "inputSchema": { "properties": { "input_files": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" } }, "required": [ "input_files", "refgene_bed", "out_prefix" ] } }, { "name": "rseqc_infer_experiment", "description": "Infer the strand specificity of RNA-seq data.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "sample_size": { "type": "number", "description": "", "default": 200000 }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file", "refgene_bed" ] } }, { "name": "rseqc_inner_distance", "description": "Calculate the inner distance (or insert size) between read pairs.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "sample_size": { "type": "number", "description": "", "default": 1000000 }, "mapq": { "type": "number", "description": "", "default": 30 }, "lower_bound": { "type": "number", "description": "", "default": -250 }, "upper_bound": { "type": "number", "description": "", "default": 250 }, "step": { "type": "number", "description": "", "default": 5 } }, "required": [ "input_file", "refgene_bed", "out_prefix" ] } }, { "name": "rseqc_junction_annotation", "description": "Compare detected splice junctions to reference gene model.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file", "refgene_bed", "out_prefix" ] } }, { "name": "rseqc_read_distribution", "description": "Calculate how mapped reads are distributed over genome features (CDS, UTR, Intron, etc).", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" } }, "required": [ "input_file", "refgene_bed" ] } }, { "name": "rseqc_read_duplication", "description": "Calculate read duplication rate.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file", "out_prefix" ] } }, { "name": "rseqc_tin", "description": "Calculate Transcript Integrity Number (TIN) for each gene.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "refgene_bed": { "type": "string", "description": "" }, "min_coverage": { "type": "number", "description": "", "default": 10 }, "sample_size": { "type": "number", "description": "", "default": 100 } }, "required": [ "input_file", "refgene_bed" ] } }, { "name": "rseqc_sc_bam_stat", "description": "QC scRNA-seq data: Summarizing mapping statistics.", "inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_file" ] } }, { "name": "rseqc_mismatch_profile", "description": "Calculate the distributions of mismatches across reads.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "read_align_length": { "type": "number", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "read_num": { "type": "number", "description": "", "default": 1000000 }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_bam", "read_align_length", "out_prefix" ] } }, { "name": "rseqc_insertion_profile", "description": "Calculate the distributions of insertions across reads.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "read_align_length": { "type": "number", "description": "" }, "out_prefix": { "type": "string", "description": "" }, "read_num": { "type": "number", "description": "", "default": 1000000 }, "mapq": { "type": "number", "description": "", "default": 30 } }, "required": [ "input_bam", "read_align_length", "out_prefix" ] } } ] }, { "server_dir": "mcp_rust-bio-tools", "server_name": "rust_bio_tools", "path": 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"description": "" }, "output_txt": { "type": "string", "description": "" }, "info_tags": { "type": "array", "description": "", "default": null }, "format_tags": { "type": "array", "description": "", "default": null } }, "required": [ "input_vcf", "output_txt" ] } }, { "name": "rbt_fastq_split", "description": "A linear time round-robin FASTQ splitter that splits a given FASTQ file into a given number of chunks.", "inputSchema": { "properties": { "input_fastq": { "type": "string", "description": "" }, "output_prefixes": { "type": "array", "description": "" } }, "required": [ "input_fastq", "output_prefixes" ] } }, { "name": "rbt_bam_depth", "description": "Linear time extraction of depth information from BAMs at given loci.", "inputSchema": { "properties": { "bam_files": { "type": "array", "description": "" }, "loci_bed": { "type": "string", "description": "" }, "output_depth": { "type": "string", "description": "" } }, "required": [ "bam_files", "loci_bed", "output_depth" ] } }, { "name": "rbt_fastq_filter", "description": "A utility to quickly filter records from a FASTQ file based on a list of IDs.", "inputSchema": { "properties": { "input_fastq": { "type": "string", "description": "" }, "ids_to_keep": { "type": "string", "description": "" }, "output_fastq": { "type": "string", "description": "" } }, "required": [ "input_fastq", "ids_to_keep", "output_fastq" ] } }, { "name": "rbt_collapse_reads_to_fragments", "description": "Merge BAM or FASTQ reads using marked duplicates or unique molecular identifiers (UMIs).", "inputSchema": { "properties": { "mode": { "type": "string", "description": "" }, "input_file": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "" }, "umi_len": { "type": "number", "description": "", "default": 0 } }, "required": [ "mode", "input_file", "output_file" ] } }, { "name": "rbt_vcf_report", "description": "Generate interactive HTML based reports visualizing genomics data in VCF and BAM format.", "inputSchema": { "properties": { "vcf_file": { "type": "string", "description": "" }, "outdir": { "type": "string", "description": "" }, "bam_file": { "type": "string", "description": "", "default": null }, "reference": { "type": "string", "description": "", "default": null } }, "required": [ "vcf_file", "outdir" ] } }, { "name": "rbt_csv_report", "description": "Generate an interactive HTML based report from a CSV file including visualizations.", "inputSchema": { "properties": { "csv_file": { "type": "string", "description": "" }, "outdir": { "type": "string", "description": "" }, "sep": { "type": "string", "description": "", "default": "," } }, "required": [ "csv_file", "outdir" ] } }, { "name": "rbt_vcf_split", "description": "Split VCF/BCF files into N equal chunks, including BND support.", "inputSchema": { "properties": { "input_vcf": { "type": "string", "description": "" }, "output_vcfs": { "type": "array", "description": "" } }, "required": [ "input_vcf", "output_vcfs" ] } }, { "name": "rbt_plot_bam", "description": "Generate visualizations for a specific region of one or multiple BAM files with a given reference.", "inputSchema": { "properties": { "bam_files": { "type": "array", "description": "" }, "reference": { "type": "string", "description": "" }, "region": { "type": "string", "description": "" }, "output_html": { "type": "string", "description": "" } }, "required": [ "bam_files", "reference", "region", "output_html" ] } } ] }, { "server_dir": "mcp_sage-proteomics", "server_name": "sage_proteomics", "path": "/225040511/project/Biomni/mcp_generated/mcp_sage-proteomics", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_sage-proteomics/app/sage-proteomics_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_sage-proteomics/app/sage-proteomics_server.py", "tool_count": 1, "tools": [ { "name": "sage_search", "description": "Runs a Sage proteomics search, dynamically generating the required JSON configuration.", "inputSchema": { "properties": { "mzml_paths": { "type": "array", "description": "" }, "fasta": { "type": "string", "description": "" }, "output_directory": { "type": "string", "description": "", "default": null }, "peptide_fdr": { "type": "number", "description": "", "default": 0.01 }, "protein_fdr": { "type": "number", "description": "", "default": 0.01 }, "report_psms": { "type": "number", "description": "", "default": 1 }, "chimera": { "type": "boolean", "description": "", "default": false }, "min_ion_index": { "type": "number", "description": "", "default": 2 }, "db_bucket": { "type": "string", "description": "", "default": null }, "missed_cleavages": { "type": "number", "description": "", "default": 0 }, "fragment_min_mz": { "type": "number", "description": "", "default": 200.0 }, "fragment_max_mz": { "type": "number", "description": "", "default": 2000.0 }, "peptide_min_len": { "type": "number", "description": "", "default": 5 }, "peptide_max_len": { "type": "number", "description": "", "default": 50 }, "peptide_min_mass": { "type": "number", "description": "", "default": 500.0 }, "peptide_max_mass": { "type": "number", "description": "", "default": 5000.0 }, "static_mods": { "type": "number", "description": "", "default": null }, "variable_mods": { "type": "number", "description": "", "default": null }, "max_variable_mods": { "type": "number", "description": "", "default": 2 }, "enzyme_cleave_at": { "type": "string", "description": "", "default": "KR" }, "enzyme_restrict": { "type": "string", "description": "", "default": "P" }, "enzyme_c_terminal": { "type": "boolean", "description": "", "default": true }, "decoy_tag": { "type": "string", "description": "", "default": "rev_" }, "generate_decoys": { "type": "boolean", "description": "", "default": true }, "quant_tmt": { "type": "string", "description": "", "default": null }, "quant_tmt_level": { "type": "number", "description": "", "default": 3 }, "quant_lfq": { "type": "boolean", "description": "", "default": false }, "quant_lfq_min_peptide_ratios": { "type": "number", "description": "", "default": 1 }, "quant_lfq_min_peptides": { "type": "number", "description": "", "default": 1 } }, "required": [ "mzml_paths", "fasta" ] } } ] }, { "server_dir": "mcp_samap", "server_name": "samap", "path": "/225040511/project/Biomni/mcp_generated/mcp_samap", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_samap/app/samap_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_samap/app/samap_server.py", "tool_count": 3, "tools": [ { "name": "samap_blast", "description": "Run the BLAST homology mapping step for SAMap. This generates the reciprocal", "inputSchema": { "properties": { "fasta1": { "type": "string", "description": "" }, "fasta2": { "type": "string", "description": "" }, "name1": { "type": "string", "description": "" }, "name2": { "type": "string", "description": "" }, "output_dir": { "type": "string", "description": "", "default": "maps/" }, "num_threads": { "type": "number", "description": "", "default": 1 } }, "required": [ "fasta1", "fasta2", "name1", "name2" ] } }, { "name": "samap_run", "description": "Run the SAMap algorithm to align single-cell RNA sequencing datasets from two species.", "inputSchema": { "properties": { "species1_h5ad": { "type": "string", "description": "" }, "species2_h5ad": { "type": "string", "description": "" }, "species1_name": { "type": "string", "description": "" }, "species2_name": { "type": "string", "description": "" }, "f_maps": { "type": "string", "description": "", "default": "maps/" }, "save_dir": { "type": "string", "description": "", "default": "results/" }, "n_genes": { "type": "number", "description": "", "default": 3000 }, "k": { "type": "number", "description": "", "default": 20 }, "n_iters": { "type": "number", "description": "", "default": 3 }, "weight_adj": { "type": "boolean", "description": "", "default": true } }, "required": [ "species1_h5ad", "species2_h5ad", "species1_name", "species2_name" ] } }, { "name": "samap_export_results", "description": "Export alignment scores or cross-species mapping results from a saved SAMap object.", "inputSchema": { "properties": { "samap_obj_path": { "type": "string", "description": "" }, "output_csv": { "type": "string", "description": "", "default": "alignment_scores.csv" } }, "required": [ "samap_obj_path" ] } } ] }, { "server_dir": "mcp_sambamba", "server_name": "sambamba", "path": "/225040511/project/Biomni/mcp_generated/mcp_sambamba", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"description": "", "default": false }, "sam_input": { "type": "boolean", "description": "", "default": false }, "show_progress": { "type": "boolean", "description": "", "default": false }, "compression_level": { "type": "number", "description": "", "default": null }, "output_filename": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_file" ] } }, { "name": "index", "description": "Builds a BAI index for a BAM file.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "output_bai": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam" ] } }, { "name": "merge", "description": "Merges multiple BAM files into a single BAM 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"input_bam": { "type": "string", "description": "" }, "bed_file": { "type": "string", "description": "" }, "output_bam": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam", "bed_file" ] } }, { "name": "markdup", "description": "Marks or removes duplicate reads in a BAM file.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "output_bam": { "type": "string", "description": "" }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam", "output_bam" ] } }, { "name": "subsample", "description": "Subsamples a BAM file by a given fraction.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "fraction": { "type": "number", "description": "" }, "output_bam": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam", "fraction" ] } }, { "name": "flagstat", "description": "Outputs statistics (flagstat) for a BAM file.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam" ] } }, { "name": "depth", "description": "Outputs coverage statistics (depth) for a BAM file.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam" ] } }, { "name": "validate", "description": "Performs a simple validation check on a BAM file.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam" ] } }, { "name": "mpileup", "description": "Performs parallel execution of samtools mpileup.", "inputSchema": { "properties": { "input_bam": { "type": "string", "description": "" }, "output_file": { "type": "string", "description": "", "default": null }, "nthreads": { "type": "number", "description": "", "default": 1 }, "quiet": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_bam" ] } } ] }, { "server_dir": "mcp_samblaster", "server_name": "samblaster", "path": "/225040511/project/Biomni/mcp_generated/mcp_samblaster", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"inputSchema": { "properties": { "input_file": { "type": "string", "description": "" }, "show_rid": { "type": "boolean", "description": "", "default": false }, "show_hdr": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_file" ] } } ] }, { "server_dir": "mcp_snakemake", "server_name": "snakemake", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakemake", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snakemake/app/snakemake_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakemake/app/snakemake_server.py", "tool_count": 6, "tools": [ { "name": "snakemake_run", "description": "Execute a Snakemake workflow.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": null }, "cores": { "type": "number", "description": "", "default": 1 }, "targets": { "type": "array", "description": "", "default": null }, "dryrun": { "type": "boolean", "description": "", "default": false }, "use_conda": { "type": "boolean", "description": "", "default": false }, "use_singularity": { "type": "boolean", "description": "", "default": false }, "config": { "type": "array", "description": "", "default": null }, "configfiles": { "type": "array", "description": "", "default": null }, "workdir": { "type": "string", "description": "", "default": null }, "forceall": { "type": "boolean", "description": "", "default": false }, "keep_going": { "type": "boolean", "description": "", "default": false }, "printshellcmds": { "type": "boolean", "description": "", "default": true }, "reason": { "type": "boolean", "description": "", "default": false }, "latency_wait": { "type": "number", "description": "", "default": 5 }, "rerun_incomplete": { "type": "boolean", "description": "", "default": true } }, "required": [] } }, { "name": "snakemake_info", "description": "Get information about the Snakemake workflow without executing it.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": null }, "mode": { "type": "string", "description": "", "default": "list" } }, "required": [] } }, { "name": "snakemake_visualize", "description": "Generate a visualization of the workflow (DAG or Rulegraph) in DOT format.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": null }, "graph_type": { "type": "string", "description": "", "default": "dag" }, "output_file": { "type": "string", "description": "", "default": "workflow.dot" }, "targets": { "type": "array", "description": "", "default": null } }, "required": [] } }, { "name": "snakemake_report", "description": "Create an HTML report containing results and statistics.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": null }, "report_path": { "type": "string", "description": "", "default": "report.html" }, "config": { "type": "array", "description": "", "default": null } }, "required": [] } }, { "name": "snakemake_management", "description": "Perform maintenance tasks on the Snakemake working directory.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": null }, "unlock": { "type": "boolean", "description": "", "default": false }, "cleanup_metadata": { "type": "array", "description": "", "default": null }, "cleanup_shadow": { "type": "boolean", "description": "", "default": false } }, "required": [] } }, { "name": "snakemake_archive", "description": "Archive the workflow into a tarball, including all input files and software environment.", "inputSchema": { "properties": { "output_file": { "type": "string", "description": "" }, "snakefile": { "type": "string", "description": "", "default": null } }, "required": [ "output_file" ] } } ] }, { "server_dir": "mcp_snakemake-interface-executor-plugins", "server_name": "snakemake_interface_executor_plugins", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-executor-plugins", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-executor-plugins/app/snakemake-interface-executor-plugins_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-executor-plugins/app/snakemake-interface-executor-plugins_server.py", "tool_count": 1, "tools": [ { "name": "snakemake_interface_executor_plugins_info", "description": "Provides information about the snakemake-interface-executor-plugins package.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_snakemake-interface-report-plugins", "server_name": "snakemake_interface_report_plugins", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-report-plugins", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-report-plugins/app/snakemake-interface-report-plugins_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-report-plugins/app/snakemake-interface-report-plugins_server.py", "tool_count": 5, "tools": [ { "name": "list_snakemake_report_plugins", "description": "List all currently installed Snakemake report plugins.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "get_snakemake_report_plugin_info", "description": "Get detailed information about a specific Snakemake report plugin.", "inputSchema": { "properties": { "plugin_name": { "type": "string", "description": "" } }, "required": [ "plugin_name" ] } }, { "name": "validate_snakemake_report_plugin_settings", "description": "Validate a set of settings against a Snakemake report plugin's requirements.", "inputSchema": { "properties": { "plugin_name": { "type": "string", "description": "" }, "settings_json": 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"/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-storage-plugins/app/snakemake-interface-storage-plugins_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-interface-storage-plugins/app/snakemake-interface-storage-plugins_server.py", "tool_count": 5, "tools": [ { "name": "list_snakemake_storage_plugins", "description": "Lists all currently installed Snakemake storage plugins available in the environment.", "inputSchema": { "properties": {}, "required": [] } }, { "name": "get_storage_plugin_help", "description": "Retrieves detailed help and available settings for a specific Snakemake storage plugin.", "inputSchema": { "properties": { "plugin_name": { "type": "string", "description": "" } }, "required": [ "plugin_name" ] } }, { "name": "generate_storage_plugin_skeleton", "description": "Generates a Python code skeleton for a new Snakemake storage plugin based on the", "inputSchema": { "properties": { "output_directory": { "type": "string", "description": "" }, "plugin_name": { "type": "string", "description": "" }, "include_read_write": { "type": "boolean", "description": "", "default": true }, "include_glob": { "type": "boolean", "description": "", "default": true }, "include_touch": { "type": "boolean", "description": "", "default": true } }, "required": [ "output_directory", "plugin_name" ] } }, { "name": "validate_storage_query", "description": "Validates a storage query string against a specific installed storage plugin", "inputSchema": { "properties": { "plugin_module": { "type": "string", "description": "" }, "query": { "type": "string", "description": "" } }, "required": [ "plugin_module", "query" ] } }, { "name": "check_storage_interface_version", "description": "Checks the version of the snakemake-interface-storage-plugins package", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_snakemake-minimal", "server_name": "snakemake_minimal", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-minimal", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snakemake-minimal/app/snakemake-minimal_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-minimal/app/snakemake-minimal_server.py", "tool_count": 8, "tools": [ { "name": "snakemake_run", "description": "Execute a Snakemake workflow.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": "Snakefile" }, "cores": { "type": "number", "description": "", "default": 1 }, "targets": { "type": "array", "description": "", "default": null }, "dry_run": { "type": "boolean", "description": "", "default": false }, "force_all": { "type": "boolean", "description": "", "default": false }, "config": { "type": "array", "description": "", "default": null }, "configfiles": { "type": "array", "description": "", "default": null }, "workdir": { "type": 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potential issues and best practice violations.", "inputSchema": { "properties": { "snakefile": { "type": "string", "description": "", "default": "Snakefile" } }, "required": [] } }, { "name": "snakemake_archive", "description": "Archive the workflow (code and configuration) into a tarball.", "inputSchema": { "properties": { "output_tar": { "type": "string", "description": "", "default": "workflow_archive.tar.gz" }, "snakefile": { "type": "string", "description": "", "default": "Snakefile" } }, "required": [] } }, { "name": "snakemake_version", "description": "Get the version of the installed Snakemake.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_snakemake-wrapper-utils", "server_name": "snakemake_wrapper_utils", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakemake-wrapper-utils", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", 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"default": "" }, "parse_threads": { "type": "boolean", "description": "", "default": true }, "parse_mem": { "type": "boolean", "description": "", "default": true } }, "required": [] } }, { "name": "get_bcftools_opts", "description": "Construct bcftools options for threads (--threads) and memory (--max-mem).", "inputSchema": { "properties": { "threads": { "type": "number", "description": "", "default": 1 }, "mem_mb": { "type": "number", "description": "", "default": 2048 }, "extra": { "type": "string", "description": "", "default": "" }, "parse_threads": { "type": "boolean", "description": "", "default": true }, "parse_mem": { "type": "boolean", "description": "", "default": true } }, "required": [] } }, { "name": "get_vcf_type", "description": "Determine the VCF format (VCF, VCF.GZ, or BCF) based on the file extension.", "inputSchema": { "properties": { "output_file": { "type": "string", "description": "" } }, "required": [ "output_file" ] } }, { "name": "parse_mem_to_mb", "description": "Convert a memory string (e.g., '8G', '512M', '1024') into Megabytes (int).", "inputSchema": { "properties": { "mem_string": { "type": "string", "description": "" } }, "required": [ "mem_string" ] } } ] }, { "server_dir": "mcp_snakesv", "server_name": "snakesv", "path": "/225040511/project/Biomni/mcp_generated/mcp_snakesv", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snakesv/app/snakesv_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snakesv/app/snakesv_server.py", "tool_count": 4, "tools": [ { "name": "snakesv_run", "description": "Execute the snakeSV pipeline for structural variant (SV) discovery and analysis.", "inputSchema": { "properties": { "config_file": { "type": "string", "description": "" }, "cores": { "type": "number", "description": "", "default": 1 }, "workdir": { "type": "string", "description": "", "default": null }, "use_conda": { "type": "boolean", "description": "", "default": true }, "dry_run": { "type": "boolean", "description": "", "default": false }, "unlock": { "type": "boolean", "description": "", "default": false }, "rerun_incomplete": { "type": "boolean", "description": "", "default": true }, "latency_wait": { "type": "number", "description": "", "default": 5 }, "additional_args": { "type": "string", "description": "", "default": null } }, "required": [ "config_file" ] } }, { "name": "snakesv_test_run", "description": "Run the snakeSV pipeline using the built-in example dataset to verify the installation.", "inputSchema": { "properties": { "output_directory": { "type": "string", "description": "" } }, "required": [ "output_directory" ] } }, { "name": "snakesv_cluster_submit", "description": "Submit the snakeSV pipeline to a high-performance computing (HPC) cluster using snakejob.", "inputSchema": { "properties": { "config_file": { "type": "string", "description": "" }, "cluster_config": { "type": "string", "description": "" }, "jobs": { "type": "number", "description": "", "default": 10 }, "workdir": { "type": "string", "description": "", "default": null }, "additional_args": { "type": "string", "description": "", "default": null } }, "required": [ "config_file", "cluster_config" ] } }, { "name": "snakesv_help", "description": "Display the help information for the snakeSV command-line tool.", "inputSchema": { "properties": {}, "required": [] } } ] }, { "server_dir": "mcp_snippy", "server_name": "snippy", "path": "/225040511/project/Biomni/mcp_generated/mcp_snippy", "command": [ "/225040511/miniconda3/envs/biomni_e1/bin/python", "/225040511/project/Biomni/mcp_generated/mcp_snippy/app/snippy_shim_server.py" ], "metadata_source": "/225040511/project/Biomni/mcp_generated/mcp_snippy/app/snippy_server.py", "tool_count": 5, "tools": [ { "name": "snippy", "description": "Rapid bacterial SNP calling and core genome alignments.", "inputSchema": { "properties": { "outdir": { "type": "string", "description": "" }, "reference": { "type": "string", "description": "" }, "cpus": { "type": "number", "description": "", "default": 1 }, "r1": { "type": "string", "description": "", "default": null }, "r2": { "type": "string", "description": "", "default": null }, "contigs_file": { "type": "string", "description": "", "default": null }, "rgid": { "type": "string", "description": "", "default": null }, "mapqual": { "type": "number", "description": "", "default": 60 }, "basequal": { "type": "number", "description": "", "default": 13 }, "maxsoft": { "type": "number", "description": "", "default": 10 }, "mincov": { "type": "number", "description": "", "default": 10 }, "minfrac": { "type": "number", "description": "", "default": 0.9 }, "minqual": { "type": "number", "description": "", "default": 100 }, "targets": { "type": "string", "description": "", "default": null }, "mask": { "type": "string", "description": "", "default": null }, "cleanup": { "type": "boolean", "description": "", "default": false }, "subsample": { "type": "number", "description": "", "default": null }, "unmapped": { "type": "boolean", "description": "", "default": false }, "report": { "type": "boolean", "description": "", "default": false } }, "required": [ "outdir", "reference" ] } }, { "name": "snippy_core", "description": "Generates a core SNP alignment from multiple Snippy output folders.", "inputSchema": { "properties": { "snippy_folders": { "type": "array", "description": "" }, "prefix": { "type": "string", "description": "", "default": "core" }, "reference": { "type": "string", "description": "", "default": null }, "aformat": { "type": "string", "description": "", "default": "fasta" }, "mask": { "type": "string", "description": "", "default": null }, "mincov": { "type": "number", "description": "", "default": 10 }, "minqual": { "type": "number", "description": "", "default": 100 } }, "required": [ "snippy_folders" ] } }, { "name": "snippy_vcf_report", "description": "Generates a detailed report for variants in a Snippy VCF file.", "inputSchema": { "properties": { "snippy_output_dir": { "type": "string", "description": "" }, "cpus": { "type": "number", "description": "", "default": 1 }, "auto": { "type": "boolean", "description": "", "default": true }, "html": { "type": "boolean", "description": "", "default": false }, "vcf_file": { "type": "string", "description": "", "default": null }, "bam_file": { "type": "string", "description": "", "default": null } }, "required": [ "snippy_output_dir" ] } }, { "name": "snippy_multi", "description": "Simplifies running a set of isolate sequences against the same reference,", "inputSchema": { "properties": { "input_tab_file": { "type": "string", "description": "" }, "reference": { "type": "string", "description": "" }, "cpus": { "type": "number", "description": "", "default": 1 }, "outdir_base": { "type": "string", "description": "" }, "mapqual": { "type": "number", "description": "", "default": 60 }, "basequal": { "type": "number", "description": "", "default": 13 }, "maxsoft": { "type": "number", "description": "", "default": 10 }, "mincov": { "type": "number", "description": "", "default": 10 }, "minfrac": { "type": "number", "description": "", "default": 0.9 }, "minqual": { "type": "number", "description": "", "default": 100 }, "targets": { "type": "string", "description": "", "default": null }, "mask": { "type": "string", "description": "", "default": null }, "cleanup": { "type": "boolean", "description": "", "default": false }, "subsample": { "type": "number", "description": "", "default": null }, "unmapped": { "type": "boolean", "description": "", "default": false }, "report": { "type": "boolean", "description": "", "default": false } }, "required": [ "input_tab_file", "reference" ] } }, { "name": "snippy_clean_full_aln", "description": "Cleans a core.full.aln file by replacing 'weird' characters with 'N'.", "inputSchema": { "properties": { "full_alignment_file": { "type": "string", "description": "" } }, "required": [ 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