tooluniverse 1.0.10__py3-none-any.whl → 1.0.11.1__py3-none-any.whl

tooluniverse/data/cbioportal_tools.json

@@ -0,0 +1,87 @@
+[
+  {
+    "type": "CBioPortalRESTTool",
+    "name": "cBioPortal_get_cancer_studies",
+    "description": "Get list of cancer studies from cBioPortal",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "limit": {"type": "integer", "default": 20, "description": "Number of studies to return"}
+      }
+    },
+    "fields": {
+      "endpoint": "https://www.cbioportal.org/api/studies?limit={limit}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "studyId": {"type": "string"},
+          "name": {"type": "string"},
+          "description": {"type": "string"},
+          "cancerTypeId": {"type": "string"},
+          "publicStudy": {"type": "boolean"},
+          "pmid": {"type": "string"},
+          "citation": {"type": "string"},
+          "groups": {"type": "array"},
+          "status": {"type": "string"},
+          "importDate": {"type": "string"},
+          "allSampleCount": {"type": "integer"},
+          "readPermission": {"type": "boolean"},
+          "referenceGenome": {"type": "string"}
+        }
+      }
+    },
+    "test_examples": [{"limit": 5}, {"limit": 10}]
+  },
+  {
+    "type": "CBioPortalRESTTool",
+    "name": "cBioPortal_get_mutations",
+    "description": "Get mutation data for specific genes in a cancer study",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "study_id": {"type": "string", "description": "Cancer study ID"},
+        "gene_list": {"type": "string", "description": "Comma-separated gene symbols"}
+      },
+      "required": ["study_id", "gene_list"]
+    },
+    "fields": {
+      "endpoint": "https://www.cbioportal.org/api/mutations?studyId={study_id}&geneList={gene_list}",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "sampleId": {"type": "string"},
+          "studyId": {"type": "string"},
+          "geneSymbol": {"type": "string"},
+          "mutationType": {"type": "string"},
+          "proteinChange": {"type": "string"},
+          "aminoAcidChange": {"type": "string"},
+          "chromosome": {"type": "string"},
+          "startPosition": {"type": "integer"},
+          "endPosition": {"type": "integer"},
+          "referenceAllele": {"type": "string"},
+          "variantAllele": {"type": "string"},
+          "mutationStatus": {"type": "string"},
+          "validationStatus": {"type": "string"},
+          "sequencingCenter": {"type": "string"},
+          "sequencer": {"type": "string"},
+          "tumorSeqAllele1": {"type": "string"},
+          "tumorSeqAllele2": {"type": "string"},
+          "matchedNormSampleBarcode": {"type": "string"},
+          "tumorSampleBarcode": {"type": "string"}
+        }
+      }
+    },
+    "test_examples": [
+      {"study_id": "brca_tcga", "gene_list": "BRCA1,BRCA2"},
+      {"study_id": "luad_tcga", "gene_list": "EGFR,KRAS"}
+    ]
+  }
+]

tooluniverse/data/clinvar_tools.json

@@ -0,0 +1,235 @@
+[
+  {
+    "type": "ClinVarSearchVariants",
+    "name": "clinvar_search_variants",
+    "description": "Search for variants in ClinVar database by gene name, condition, or variant ID. Returns variant identifiers and basic information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene": {
+          "type": "string",
+          "description": "Gene name or symbol (e.g., 'BRCA1', 'BRCA2')"
+        },
+        "condition": {
+          "type": "string",
+          "description": "Disease or condition name (e.g., 'breast cancer', 'diabetes')"
+        },
+        "variant_id": {
+          "type": "string",
+          "description": "ClinVar variant ID (e.g., '12345')"
+        },
+        "max_results": {
+          "type": "integer",
+          "description": "Maximum number of results to return",
+          "default": 20,
+          "minimum": 1,
+          "maximum": 100
+        }
+      },
+      "required": []
+    },
+    "fields": {
+      "endpoint": "/esearch.fcgi",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "ClinVar search results",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Search results from ClinVar",
+          "properties": {
+            "esearchresult": {
+              "type": "object",
+              "properties": {
+                "count": {
+                  "type": "string",
+                  "description": "Number of results found"
+                },
+                "idlist": {
+                  "type": "array",
+                  "items": {
+                    "type": "string"
+                  },
+                  "description": "List of ClinVar variant IDs"
+                },
+                "querytranslation": {
+                  "type": "string",
+                  "description": "Translated query"
+                }
+              }
+            }
+          }
+        },
+        "search_params": {
+          "type": "object",
+          "description": "Search parameters used",
+          "properties": {
+            "gene": {"type": "string"},
+            "condition": {"type": "string"},
+            "variant_id": {"type": "string"}
+          }
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "gene": "BRCA1",
+        "max_results": 10
+      },
+      {
+        "condition": "breast cancer",
+        "max_results": 5
+      }
+    ],
+    "label": [
+      "ClinVar",
+      "Variants",
+      "Search"
+    ],
+    "metadata": {
+      "tags": ["variants", "clinical", "disease"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "ClinVarGetVariantDetails",
+    "name": "clinvar_get_variant_details",
+    "description": "Get detailed variant information from ClinVar by variant ID. Returns comprehensive variant data including clinical significance.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "variant_id": {
+          "type": "string",
+          "description": "ClinVar variant ID (e.g., '12345', '123456')"
+        }
+      },
+      "required": ["variant_id"]
+    },
+    "fields": {
+      "endpoint": "/efetch.fcgi",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "ClinVar variant details",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Detailed variant information from ClinVar",
+          "properties": {
+            "variation": {
+              "type": "object",
+              "description": "Variant data structure"
+            }
+          }
+        },
+        "variant_id": {
+          "type": "string",
+          "description": "Input variant ID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "variant_id": "12345"
+      },
+      {
+        "variant_id": "123456"
+      }
+    ],
+    "label": [
+      "ClinVar",
+      "Variant",
+      "Details"
+    ],
+    "metadata": {
+      "tags": ["variant", "details", "clinical"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "ClinVarGetClinicalSignificance",
+    "name": "clinvar_get_clinical_significance",
+    "description": "Get clinical significance information for a variant from ClinVar. Returns pathogenicity classification and clinical interpretations.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "variant_id": {
+          "type": "string",
+          "description": "ClinVar variant ID (e.g., '12345', '123456')"
+        }
+      },
+      "required": ["variant_id"]
+    },
+    "fields": {
+      "endpoint": "/esummary.fcgi",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "ClinVar clinical significance data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Clinical significance information from ClinVar",
+          "properties": {
+            "result": {
+              "type": "object",
+              "description": "Summary results for the variant"
+            }
+          }
+        },
+        "variant_id": {
+          "type": "string",
+          "description": "Input variant ID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "variant_id": "12345"
+      },
+      {
+        "variant_id": "123456"
+      }
+    ],
+    "label": [
+      "ClinVar",
+      "Clinical",
+      "Significance"
+    ],
+    "metadata": {
+      "tags": ["clinical", "pathogenicity", "significance"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  }
+]

tooluniverse/data/compose_tools.json

@@ -40,95 +40,6 @@
     "composition_file": "drug_safety_analyzer.py",
     "composition_function": "compose"
   },
-  {
-    "type": "ComposeTool",
-    "name": "ToolDescriptionOptimizer",
-    "description": "Optimizes a tool's description and parameter descriptions by generating test cases, executing them, analyzing the results, and suggesting improved descriptions for both the tool and its arguments. Optionally saves a comprehensive optimization report to a file without overwriting the original.",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "tool_config": {
-          "type": "object",
-          "description": "The full configuration of the tool to optimize."
-        },
-        "save_to_file": {
-          "type": "boolean",
-          "description": "If true, save the optimized description to a file (do not overwrite the original).",
-          "default": false
-        },
-        "output_file": {
-          "type": "string",
-          "description": "Optional file path to save the optimized description. If not provided, use '<tool_name>_optimized_description.txt'."
-        },
-        "max_iterations": {
-          "type": "integer",
-          "description": "Maximum number of optimization rounds to perform.",
-          "default": 3
-        },
-        "satisfaction_threshold": {
-          "type": "number",
-          "description": "Quality score threshold (1-10) to consider optimization satisfactory.",
-          "default": 8
-        }
-      },
-      "required": [
-        "tool_config",
-        "save_to_file",
-        "output_file",
-        "max_iterations",
-        "satisfaction_threshold"
-      ]
-    },
-    "auto_load_dependencies": true,
-    "fail_on_missing_tools": false,
-    "required_tools": [
-      "TestCaseGenerator",
-      "DescriptionAnalyzer",
-      "ArgumentDescriptionOptimizer",
-      "DescriptionQualityEvaluator"
-    ],
-    "composition_file": "tool_description_optimizer.py",
-    "composition_function": "compose"
-  },
-  {
-    "type": "ComposeTool",
-    "name": "ToolDiscover",
-    "description": "Generates new ToolUniverse-compliant tools based on short descriptions through an intelligent discovery and refinement process. Automatically determines the optimal tool type and category, discovers similar existing tools, generates initial specifications, and iteratively refines the tool configuration using agentic optimization tools until it meets quality standards.",
-    "parameter": {
-      "type": "object",
-      "properties": {
-        "tool_description": {
-          "type": "string",
-          "description": "Short description of the desired tool functionality and purpose. Tool Discover will automatically analyze this to determine the optimal tool type (PackageTool, RESTTool, XMLTool, or AgenticTool) and appropriate category."
-        },
-        "max_iterations": {
-          "type": "integer",
-          "description": "Maximum number of refinement iterations to perform.",
-          "default": 20
-        },
-        "save_to_file": {
-          "type": "boolean",
-          "description": "Whether to save the generated tool configuration and report to a file.",
-          "default": true
-        },
-        "output_file": {
-          "type": "string",
-          "description": "Optional file path to save the generated tool. If not provided, uses auto-generated filename."
-        }
-      },
-      "required": [
-        "tool_description",
-        "max_iterations",
-        "save_to_file",
-        "output_file"
-      ]
-    },
-    "auto_load_dependencies": true,
-    "fail_on_missing_tools": false,
-    "required_tools": [],
-    "composition_file": "tool_discover.py",
-    "composition_function": "compose"
-  },
   {
     "type": "ComposeTool",
     "name": "LiteratureSearchTool",

tooluniverse/data/dbsnp_tools.json

@@ -0,0 +1,275 @@
+[
+  {
+    "type": "dbSNPGetVariantByRsID",
+    "name": "dbsnp_get_variant_by_rsid",
+    "description": "Get variant information from dbSNP by rsID. Returns genomic coordinates, alleles, and basic variant information.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "rsid": {
+          "type": "string",
+          "description": "dbSNP rsID (e.g., 'rs12345', '12345')"
+        }
+      },
+      "required": ["rsid"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP variant information",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Variant information from dbSNP",
+          "properties": {
+            "refsnp_id": {
+              "type": "string",
+              "description": "dbSNP reference ID"
+            },
+            "primary_snapshot_data": {
+              "type": "object",
+              "description": "Primary variant data",
+              "properties": {
+                "placements_with_allele": {
+                  "type": "array",
+                  "description": "Genomic placements",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "seq_id": {
+                        "type": "string",
+                        "description": "Chromosome"
+                      },
+                      "position": {
+                        "type": "integer",
+                        "description": "Genomic position"
+                      },
+                      "alleles": {
+                        "type": "array",
+                        "description": "Allele information"
+                      }
+                    }
+                  }
+                }
+              }
+            }
+          }
+        },
+        "rsid": {
+          "type": "string",
+          "description": "Input rsID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "rsid": "rs12345"
+      },
+      {
+        "rsid": "rs429358"
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Variant",
+      "RsID"
+    ],
+    "metadata": {
+      "tags": ["snp", "variant", "genomics"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  },
+  {
+    "type": "dbSNPSearchByGene",
+    "name": "dbsnp_search_by_gene",
+    "description": "Search for variants in a specific gene. Returns variants associated with the gene symbol.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "gene_symbol": {
+          "type": "string",
+          "description": "Gene symbol (e.g., 'BRCA1', 'TP53', 'APOE')"
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of results to return",
+          "default": 20,
+          "minimum": 1,
+          "maximum": 100
+        }
+      },
+      "required": ["gene_symbol"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP gene search results",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Search results from dbSNP",
+          "properties": {
+            "variants": {
+              "type": "array",
+              "description": "Array of variant information",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "refsnp_id": {
+                    "type": "string",
+                    "description": "dbSNP reference ID"
+                  },
+                  "gene": {
+                    "type": "string",
+                    "description": "Gene symbol"
+                  },
+                  "position": {
+                    "type": "integer",
+                    "description": "Genomic position"
+                  }
+                }
+              }
+            }
+          }
+        },
+        "gene_symbol": {
+          "type": "string",
+          "description": "Input gene symbol"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "gene_symbol": "BRCA1",
+        "limit": 10
+      },
+      {
+        "gene_symbol": "TP53",
+        "limit": 5
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Gene",
+      "Search"
+    ],
+    "metadata": {
+      "tags": ["gene", "search", "variants"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 3 seconds"
+    }
+  },
+  {
+    "type": "dbSNPGetFrequencies",
+    "name": "dbsnp_get_frequencies",
+    "description": "Get allele frequencies for a variant from dbSNP. Returns population-specific allele frequency data.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "rsid": {
+          "type": "string",
+          "description": "dbSNP rsID (e.g., 'rs12345', '12345')"
+        }
+      },
+      "required": ["rsid"]
+    },
+    "fields": {
+      "endpoint": "/beta/refsnp",
+      "return_format": "JSON"
+    },
+    "return_schema": {
+      "type": "object",
+      "description": "dbSNP allele frequency data",
+      "properties": {
+        "status": {
+          "type": "string",
+          "description": "Status of the request"
+        },
+        "data": {
+          "type": "object",
+          "description": "Variant information from dbSNP",
+          "properties": {
+            "refsnp_id": {
+              "type": "string",
+              "description": "dbSNP reference ID"
+            },
+            "primary_snapshot_data": {
+              "type": "object",
+              "description": "Primary variant data"
+            }
+          }
+        },
+        "frequencies": {
+          "type": "array",
+          "description": "Array of allele frequency data",
+          "items": {
+            "type": "object",
+            "properties": {
+              "population": {
+                "type": "string",
+                "description": "Population name"
+              },
+              "allele": {
+                "type": "string",
+                "description": "Allele"
+              },
+              "frequency": {
+                "type": "number",
+                "description": "Allele frequency"
+              }
+            }
+          }
+        },
+        "rsid": {
+          "type": "string",
+          "description": "Input rsID"
+        },
+        "url": {
+          "type": "string",
+          "description": "API URL used"
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "rsid": "rs429358"
+      },
+      {
+        "rsid": "rs7412"
+      }
+    ],
+    "label": [
+      "dbSNP",
+      "Frequency",
+      "Population"
+    ],
+    "metadata": {
+      "tags": ["frequency", "population", "allele"],
+      "difficulty_level": "easy",
+      "estimated_execution_time": "< 2 seconds"
+    }
+  }
+]