tooluniverse 1.0.11.1__py3-none-any.whl → 1.0.12__py3-none-any.whl

tooluniverse/data/gdc_tools.json

@@ -0,0 +1,116 @@
+[
+  {
+    "name": "GDC_search_cases",
+    "type": "GDCCasesTool",
+    "description": "Search cancer cohort cases in NCI GDC by project and filters. Use to retrieve case-level metadata for cohort construction and downstream file queries.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "project_id": {
+          "type": "string",
+          "description": "GDC project identifier (e.g., 'TCGA-BRCA')."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of results (1–100)."
+        },
+        "offset": {
+          "type": "integer",
+          "default": 0,
+          "minimum": 0,
+          "description": "Offset for pagination (0-based)."
+        }
+      }
+    },
+    "fields": {
+      "endpoint": "https://api.gdc.cancer.gov/cases",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "GDC cases response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "hits": {
+              "type": "array",
+              "items": {"type": "object"}
+            },
+            "pagination": {"type": "object"}
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"project_id": "TCGA-BRCA", "size": 1}
+    ],
+    "label": ["GDC", "Cases", "Oncogenomics"],
+    "metadata": {
+      "tags": ["oncogenomics", "cohort", "cases"],
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "name": "GDC_list_files",
+    "type": "GDCFilesTool",
+    "description": "List GDC files filtered by data_type and other fields. Use to identify downloadable artifacts (e.g., expression quantification) for analysis pipelines.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "data_type": {
+          "type": "string",
+          "description": "Data type filter (e.g., 'Gene Expression Quantification')."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of results (1–100)."
+        },
+        "offset": {
+          "type": "integer",
+          "default": 0,
+          "minimum": 0,
+          "description": "Offset for pagination (0-based)."
+        }
+      }
+    },
+    "fields": {
+      "endpoint": "https://api.gdc.cancer.gov/files",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "GDC files response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "hits": {
+              "type": "array",
+              "items": {"type": "object"}
+            },
+            "pagination": {"type": "object"}
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"data_type": "Gene Expression Quantification", "size": 1}
+    ],
+    "label": ["GDC", "Files", "Oncogenomics"],
+    "metadata": {
+      "tags": ["downloads", "files", "expression"],
+      "estimated_execution_time": "< 3 seconds"
+    }
+  }
+]

tooluniverse/data/gtex_tools.json

@@ -0,0 +1,116 @@
+[
+  {
+    "name": "GTEx_get_expression_summary",
+    "type": "GTExExpressionTool",
+    "description": "Summarize tissue-specific expression (e.g., median TPM) for a gene across GTEx tissues. Use to profile baseline expression patterns for targets/biomarkers.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "ensembl_gene_id": {
+          "type": "string",
+          "description": "Ensembl gene identifier (e.g., 'ENSG00000141510' for TP53)."
+        }
+      },
+      "required": ["ensembl_gene_id"]
+    },
+    "fields": {
+      "endpoint": "https://gtexportal.org/api/v2/expression/geneExpression",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "GTEx expression summary response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "geneExpression": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "tissueSiteDetailId": {"type": "string"},
+                  "median": {"type": "number"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"ensembl_gene_id": "ENSG00000141510"}
+    ],
+    "label": ["GTEx", "Expression", "Summary"],
+    "metadata": {
+      "tags": ["expression", "tissue", "baseline"],
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "name": "GTEx_query_eqtl",
+    "type": "GTExEQTLTool",
+    "description": "Query GTEx single-tissue eQTL associations for a gene. Use to identify regulatory variants (variantId, pValue, slope) relevant to expression regulation.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "ensembl_gene_id": {
+          "type": "string",
+          "description": "Ensembl gene identifier (e.g., 'ENSG00000141510')."
+        },
+        "page": {
+          "type": "integer",
+          "default": 1,
+          "minimum": 1,
+          "description": "Page number (1-based)."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of records per page (1–100)."
+        }
+      },
+      "required": ["ensembl_gene_id"]
+    },
+    "fields": {
+      "endpoint": "https://gtexportal.org/api/v2/association/singleTissueEqtl",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "GTEx eQTL query response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "singleTissueEqtl": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "variantId": {"type": "string"},
+                  "pValue": {"type": "number"},
+                  "slope": {"type": "number"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"ensembl_gene_id": "ENSG00000141510", "page": 1, "size": 5}
+    ],
+    "label": ["GTEx", "eQTL", "Association"],
+    "metadata": {
+      "tags": ["eqtl", "variant", "regulation"],
+      "estimated_execution_time": "< 3 seconds"
+    }
+  }
+]

tooluniverse/data/mgnify_tools.json

@@ -0,0 +1,121 @@
+[
+  {
+    "name": "MGnify_search_studies",
+    "type": "MGnifyStudiesTool",
+    "description": "Search MGnify metagenomics/microbiome studies by biome/keyword. Use to discover study accessions and attributes for downstream analyses and downloads.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "biome": {
+          "type": "string",
+          "description": "Biome identifier (e.g., 'root:Host-associated')."
+        },
+        "search": {
+          "type": "string",
+          "description": "Keyword to search in study titles/descriptions."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of records per page (1–100)."
+        }
+      }
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/metagenomics/api/latest/studies",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "MGnify study list response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "data": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "id": {"type": "string"},
+                  "type": {"type": "string"},
+                  "attributes": {"type": "object"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"biome": "root:Host-associated", "size": 1}
+    ],
+    "label": ["MGnify", "Microbiome", "Study"],
+    "metadata": {
+      "tags": ["microbiome", "metagenomics", "study"],
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "name": "MGnify_list_analyses",
+    "type": "MGnifyAnalysesTool",
+    "description": "List analyses associated with a study accession (taxonomic/functional outputs). Use to enumerate available processed results for programmatic retrieval.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "study_accession": {
+          "type": "string",
+          "description": "MGnify study accession (e.g., 'MGYS00000001')."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of records per page (1–100)."
+        }
+      },
+      "required": ["study_accession"]
+    },
+    "fields": {
+      "endpoint": "https://www.ebi.ac.uk/metagenomics/api/latest/analyses",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "MGnify analyses list response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "data": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "id": {"type": "string"},
+                  "type": {"type": "string"},
+                  "attributes": {"type": "object"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"study_accession": "MGYS00000001", "size": 1}
+    ],
+    "label": ["MGnify", "Microbiome", "Analysis"],
+    "metadata": {
+      "tags": ["analysis", "taxonomy", "function"],
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]

tooluniverse/data/obis_tools.json

@@ -0,0 +1,122 @@
+[
+  {
+    "name": "OBIS_search_taxa",
+    "type": "OBISTaxaTool",
+    "description": "Resolve marine taxa in OBIS by scientific name to obtain standardized identifiers (AphiaID), ranks, and names. Use before querying marine occurrences.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "scientificname": {
+          "type": "string",
+          "description": "Scientific name query (e.g., 'Gadus')."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of records to return (1–100)."
+        }
+      },
+      "required": ["scientificname"]
+    },
+    "fields": {
+      "endpoint": "https://api.obis.org/v3/taxon",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "OBIS taxon search response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "results": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "scientificName": {"type": "string"},
+                  "aphiaID": {"type": "integer"},
+                  "rank": {"type": "string"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"scientificname": "Gadus", "size": 1}
+    ],
+    "label": ["OBIS", "Taxonomy", "Marine"],
+    "metadata": {
+      "tags": ["marine", "taxonomy", "aphia"],
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "name": "OBIS_search_occurrences",
+    "type": "OBISOccurrenceTool",
+    "description": "Retrieve marine species occurrence records (with coordinates/time) from OBIS using flexible filters. Use for ocean biodiversity distribution analyses.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "scientificname": {
+          "type": "string",
+          "description": "Scientific name filter to restrict occurrences."
+        },
+        "areaid": {
+          "type": "string",
+          "description": "Area identifier filter (per OBIS API)."
+        },
+        "size": {
+          "type": "integer",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100,
+          "description": "Number of records to return (1–100)."
+        }
+      }
+    },
+    "fields": {
+      "endpoint": "https://api.obis.org/v3/occurrence",
+      "format": "json"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "OBIS occurrence search response",
+      "properties": {
+        "status": {"type": "string"},
+        "data": {
+          "type": "object",
+          "properties": {
+            "results": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "scientificName": {"type": "string"},
+                  "decimalLatitude": {"type": "number"},
+                  "decimalLongitude": {"type": "number"},
+                  "eventDate": {"type": "string"}
+                }
+              }
+            }
+          }
+        },
+        "url": {"type": "string"}
+      }
+    },
+    "test_examples": [
+      {"size": 1}
+    ],
+    "label": ["OBIS", "Occurrence", "Marine"],
+    "metadata": {
+      "tags": ["marine", "occurrence", "geospatial"],
+      "estimated_execution_time": "< 3 seconds"
+    }
+  }
+]