Created
March 9, 2026 10:47
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BWA-MEM2 Galaxy tool parameter request schema
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| { | |
| "$defs": { | |
| "BatchDataInstance": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "src": { | |
| "enum": [ | |
| "hda", | |
| "ldda", | |
| "hdca" | |
| ], | |
| "title": "Src", | |
| "type": "string" | |
| }, | |
| "id": { | |
| "title": "Id", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "src", | |
| "id" | |
| ], | |
| "title": "BatchDataInstance", | |
| "type": "object" | |
| }, | |
| "CollectionElementCollectionRequestUri": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "class": { | |
| "const": "Collection", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "identifier": { | |
| "description": "A unique identifier for this element within the collection.", | |
| "title": "Identifier", | |
| "type": "string" | |
| }, | |
| "collection_type": { | |
| "title": "Collection Type", | |
| "type": "string" | |
| }, | |
| "elements": { | |
| "items": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/CollectionElementCollectionRequestUri" | |
| }, | |
| { | |
| "$ref": "#/$defs/CollectionElementDataRequestUri" | |
| } | |
| ] | |
| }, | |
| "title": "Elements", | |
| "type": "array" | |
| } | |
| }, | |
| "required": [ | |
| "class", | |
| "identifier", | |
| "collection_type", | |
| "elements" | |
| ], | |
| "title": "CollectionElementCollectionRequestUri", | |
| "type": "object" | |
| }, | |
| "CollectionElementDataRequestUri": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "location": { | |
| "title": "Location", | |
| "type": "string" | |
| }, | |
| "name": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Name" | |
| }, | |
| "ext": { | |
| "title": "Ext", | |
| "type": "string" | |
| }, | |
| "dbkey": { | |
| "default": "?", | |
| "title": "Dbkey", | |
| "type": "string" | |
| }, | |
| "deferred": { | |
| "default": false, | |
| "title": "Deferred", | |
| "type": "boolean" | |
| }, | |
| "created_from_basename": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Created From Basename" | |
| }, | |
| "info": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Info" | |
| }, | |
| "tags": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "type": "string" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Tags" | |
| }, | |
| "hashes": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "$ref": "#/$defs/FileHash" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Hashes" | |
| }, | |
| "space_to_tab": { | |
| "default": false, | |
| "title": "Space To Tab", | |
| "type": "boolean" | |
| }, | |
| "to_posix_lines": { | |
| "default": false, | |
| "title": "To Posix Lines", | |
| "type": "boolean" | |
| }, | |
| "class": { | |
| "const": "File", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "src": { | |
| "default": null, | |
| "title": "Src", | |
| "type": "null" | |
| }, | |
| "identifier": { | |
| "description": "A unique identifier for this element within the collection.", | |
| "title": "Identifier", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "location", | |
| "ext", | |
| "class", | |
| "identifier" | |
| ], | |
| "title": "CollectionElementDataRequestUri", | |
| "type": "object" | |
| }, | |
| "DataCollectionRequest": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "src": { | |
| "const": "hdca", | |
| "title": "Src", | |
| "type": "string" | |
| }, | |
| "id": { | |
| "title": "Id", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "src", | |
| "id" | |
| ], | |
| "title": "DataCollectionRequest", | |
| "type": "object" | |
| }, | |
| "DataRequestCollectionUri": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "class": { | |
| "const": "Collection", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "collection_type": { | |
| "title": "Collection Type", | |
| "type": "string" | |
| }, | |
| "elements": { | |
| "items": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/CollectionElementCollectionRequestUri" | |
| }, | |
| { | |
| "$ref": "#/$defs/CollectionElementDataRequestUri" | |
| } | |
| ] | |
| }, | |
| "title": "Elements", | |
| "type": "array" | |
| }, | |
| "deferred": { | |
| "default": false, | |
| "title": "Deferred", | |
| "type": "boolean" | |
| }, | |
| "name": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Name" | |
| }, | |
| "src": { | |
| "default": null, | |
| "title": "Src", | |
| "type": "null" | |
| }, | |
| "column_definitions": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "$ref": "#/$defs/SampleSheetColumnDefinition" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Column Definitions" | |
| }, | |
| "rows": { | |
| "anyOf": [ | |
| { | |
| "additionalProperties": { | |
| "items": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| }, | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ] | |
| }, | |
| "type": "array" | |
| }, | |
| "type": "object" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Rows" | |
| } | |
| }, | |
| "required": [ | |
| "class", | |
| "collection_type", | |
| "elements" | |
| ], | |
| "title": "DataRequestCollectionUri", | |
| "type": "object" | |
| }, | |
| "DataRequestHda": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "src": { | |
| "const": "hda", | |
| "default": "hda", | |
| "title": "Src", | |
| "type": "string" | |
| }, | |
| "id": { | |
| "title": "Id", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "id" | |
| ], | |
| "title": "DataRequestHda", | |
| "type": "object" | |
| }, | |
| "DataRequestLd": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "src": { | |
| "const": "ld", | |
| "deprecated": true, | |
| "title": "Src", | |
| "type": "string" | |
| }, | |
| "id": { | |
| "title": "Id", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "src", | |
| "id" | |
| ], | |
| "title": "DataRequestLd", | |
| "type": "object" | |
| }, | |
| "DataRequestLdda": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "src": { | |
| "const": "ldda", | |
| "default": "ldda", | |
| "title": "Src", | |
| "type": "string" | |
| }, | |
| "id": { | |
| "title": "Id", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "id" | |
| ], | |
| "title": "DataRequestLdda", | |
| "type": "object" | |
| }, | |
| "DataRequestUri": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "location": { | |
| "title": "Location", | |
| "type": "string" | |
| }, | |
| "name": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Name" | |
| }, | |
| "ext": { | |
| "title": "Ext", | |
| "type": "string" | |
| }, | |
| "dbkey": { | |
| "default": "?", | |
| "title": "Dbkey", | |
| "type": "string" | |
| }, | |
| "deferred": { | |
| "default": false, | |
| "title": "Deferred", | |
| "type": "boolean" | |
| }, | |
| "created_from_basename": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Created From Basename" | |
| }, | |
| "info": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Info" | |
| }, | |
| "tags": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "type": "string" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Tags" | |
| }, | |
| "hashes": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "$ref": "#/$defs/FileHash" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Hashes" | |
| }, | |
| "space_to_tab": { | |
| "default": false, | |
| "title": "Space To Tab", | |
| "type": "boolean" | |
| }, | |
| "to_posix_lines": { | |
| "default": false, | |
| "title": "To Posix Lines", | |
| "type": "boolean" | |
| }, | |
| "src": { | |
| "const": "url", | |
| "default": "url", | |
| "title": "Src", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "location", | |
| "ext" | |
| ], | |
| "title": "DataRequestUri", | |
| "type": "object" | |
| }, | |
| "FileHash": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "hash_function": { | |
| "enum": [ | |
| "MD5", | |
| "SHA-1", | |
| "SHA-256", | |
| "SHA-512" | |
| ], | |
| "title": "Hash Function", | |
| "type": "string" | |
| }, | |
| "hash_value": { | |
| "title": "Hash Value", | |
| "type": "string" | |
| } | |
| }, | |
| "required": [ | |
| "hash_function", | |
| "hash_value" | |
| ], | |
| "title": "FileHash", | |
| "type": "object" | |
| }, | |
| "SampleSheetColumnDefinition": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "name": { | |
| "title": "Name", | |
| "type": "string" | |
| }, | |
| "description": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "title": "Description" | |
| }, | |
| "type": { | |
| "enum": [ | |
| "string", | |
| "int", | |
| "float", | |
| "boolean", | |
| "element_identifier" | |
| ], | |
| "title": "Type", | |
| "type": "string" | |
| }, | |
| "optional": { | |
| "title": "Optional", | |
| "type": "boolean" | |
| }, | |
| "default_value": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| }, | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "title": "Default Value" | |
| }, | |
| "validators": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "additionalProperties": true, | |
| "type": "object" | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "title": "Validators" | |
| }, | |
| "restrictions": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| }, | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ] | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "title": "Restrictions" | |
| }, | |
| "suggestions": { | |
| "anyOf": [ | |
| { | |
| "items": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| }, | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ] | |
| }, | |
| "type": "array" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "title": "Suggestions" | |
| } | |
| }, | |
| "required": [ | |
| "name", | |
| "type", | |
| "optional" | |
| ], | |
| "title": "SampleSheetColumnDefinition", | |
| "type": "object" | |
| }, | |
| "When_algorithmic_options_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": {}, | |
| "title": "When_algorithmic_options_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_algorithmic_options_selector_do_not_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "algorithmic_options_selector": { | |
| "const": "do_not_set", | |
| "default": null, | |
| "title": "Algorithmic Options Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_algorithmic_options_selector_do_not_set", | |
| "type": "object" | |
| }, | |
| "When_algorithmic_options_selector_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "algorithmic_options_selector": { | |
| "const": "set", | |
| "default": null, | |
| "title": "Algorithmic Options Selector", | |
| "type": "string" | |
| }, | |
| "k": { | |
| "default": null, | |
| "description": "-k; default=19", | |
| "gx_type": "gx_integer", | |
| "title": "Minimum seed length", | |
| "type": "integer" | |
| }, | |
| "w": { | |
| "default": null, | |
| "description": "-w; default=100", | |
| "gx_type": "gx_integer", | |
| "title": "Band width for banded alignment", | |
| "type": "integer" | |
| }, | |
| "d": { | |
| "default": null, | |
| "description": "-d; default=100", | |
| "gx_type": "gx_integer", | |
| "title": "Off-diagonal X-dropoff", | |
| "type": "integer" | |
| }, | |
| "r": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-r; default=1.5; This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy", | |
| "gx_type": "gx_float", | |
| "title": "Look for internal seeds inside a seed longer than -k * THIS VALUE" | |
| }, | |
| "y": { | |
| "default": null, | |
| "description": "-y; default=20", | |
| "gx_type": "gx_integer", | |
| "title": "Seed occurrence for the 3rd round seeding", | |
| "type": "integer" | |
| }, | |
| "c": { | |
| "default": null, | |
| "description": "-c; default=500", | |
| "gx_type": "gx_integer", | |
| "title": "Skip seeds with more than that many occurrences", | |
| "type": "integer" | |
| }, | |
| "D": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "number" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-D; default=0.5", | |
| "gx_type": "gx_float", | |
| "title": "Drop chains shorter than this fraction of the longest overlapping chain" | |
| }, | |
| "W": { | |
| "default": null, | |
| "description": "-W; default=0", | |
| "gx_type": "gx_integer", | |
| "title": "Discard a chain if seeded bases shorter than THIS VALUE", | |
| "type": "integer" | |
| }, | |
| "m": { | |
| "default": null, | |
| "description": "-m; default=50", | |
| "gx_type": "gx_integer", | |
| "title": "Perform at most this many rounds of mate rescues for each read", | |
| "type": "integer" | |
| }, | |
| "S": { | |
| "default": null, | |
| "description": "-S", | |
| "gx_type": "gx_boolean", | |
| "title": "Skip mate rescue", | |
| "type": "boolean" | |
| }, | |
| "P": { | |
| "default": null, | |
| "description": "-P", | |
| "gx_type": "gx_boolean", | |
| "title": "Skip pairing; mate rescue performed unless -S also in use", | |
| "type": "boolean" | |
| }, | |
| "e": { | |
| "default": null, | |
| "description": "-e", | |
| "gx_type": "gx_boolean", | |
| "title": "Discard full-length exact matches", | |
| "type": "boolean" | |
| } | |
| }, | |
| "title": "When_algorithmic_options_selector_set", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": {}, | |
| "title": "When_analysis_type_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector_full": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "analysis_type_selector": { | |
| "const": "full", | |
| "default": null, | |
| "title": "Analysis Type Selector", | |
| "type": "string" | |
| }, | |
| "algorithmic_options": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__7", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Set", | |
| "selected": false, | |
| "value": "set" | |
| }, | |
| { | |
| "label": "Do not set", | |
| "selected": true, | |
| "value": "do_not_set" | |
| } | |
| ], | |
| "gx_test_help": "Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.", | |
| "gx_test_label": "Set algorithmic options?", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "scoring_options": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__8", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Set", | |
| "selected": false, | |
| "value": "set" | |
| }, | |
| { | |
| "label": "Do not set", | |
| "selected": true, | |
| "value": "do_not_set" | |
| } | |
| ], | |
| "gx_test_help": "Sets -A, -B, -O, -E, -L, and -U options.", | |
| "gx_test_label": "Set scoring options?", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "io_options": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__9", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Set", | |
| "selected": false, | |
| "value": "set" | |
| }, | |
| { | |
| "label": "Do not set", | |
| "selected": true, | |
| "value": "do_not_set" | |
| } | |
| ], | |
| "gx_test_help": "Sets -T, -h, -a, -C, -V, -Y, -M, and -K options.", | |
| "gx_test_label": "Set input/output options", | |
| "gx_type": "gx_conditional" | |
| } | |
| }, | |
| "title": "When_analysis_type_selector_full", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector_illumina": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "analysis_type_selector": { | |
| "const": "illumina", | |
| "default": null, | |
| "title": "Analysis Type Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_analysis_type_selector_illumina", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector_intractg": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "analysis_type_selector": { | |
| "const": "intractg", | |
| "default": null, | |
| "title": "Analysis Type Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_analysis_type_selector_intractg", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector_ont2d": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "analysis_type_selector": { | |
| "const": "ont2d", | |
| "default": null, | |
| "title": "Analysis Type Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_analysis_type_selector_ont2d", | |
| "type": "object" | |
| }, | |
| "When_analysis_type_selector_pacbio": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "analysis_type_selector": { | |
| "const": "pacbio", | |
| "default": null, | |
| "title": "Analysis Type Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_analysis_type_selector_pacbio", | |
| "type": "object" | |
| }, | |
| "When_do_auto_name_True": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": true, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| } | |
| }, | |
| "title": "When_do_auto_name_True", | |
| "type": "object" | |
| }, | |
| "When_fastq_input_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "fastq_input1": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__4" | |
| } | |
| ], | |
| "description": "Specify dataset with forward reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select first set of reads" | |
| }, | |
| "fastq_input2": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__5" | |
| } | |
| ], | |
| "description": "Specify dataset with reverse reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select second set of reads" | |
| }, | |
| "iset_stats": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both \"250\" and \"250,25\" will work while \"250,,10\" will not. See below for details.", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Enter mean, standard deviation, max, and min for insert lengths." | |
| } | |
| }, | |
| "required": [ | |
| "fastq_input1", | |
| "fastq_input2" | |
| ], | |
| "title": "When_fastq_input_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_fastq_input_selector_paired": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "fastq_input_selector": { | |
| "const": "paired", | |
| "default": null, | |
| "title": "Fastq Input Selector", | |
| "type": "string" | |
| }, | |
| "fastq_input1": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__2" | |
| } | |
| ], | |
| "description": "Specify dataset with forward reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select first set of reads" | |
| }, | |
| "fastq_input2": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__3" | |
| } | |
| ], | |
| "description": "Specify dataset with reverse reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select second set of reads" | |
| }, | |
| "iset_stats": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both \"250\" and \"250,25\" will work while \"250,,10\" will not. See below for details.", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Enter mean, standard deviation, max, and min for insert lengths." | |
| } | |
| }, | |
| "required": [ | |
| "fastq_input1", | |
| "fastq_input2" | |
| ], | |
| "title": "When_fastq_input_selector_paired", | |
| "type": "object" | |
| }, | |
| "When_fastq_input_selector_paired_collection": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "fastq_input_selector": { | |
| "const": "paired_collection", | |
| "default": null, | |
| "title": "Fastq Input Selector", | |
| "type": "string" | |
| }, | |
| "fastq_input1": { | |
| "anyOf": [ | |
| { | |
| "$ref": "#/$defs/DataCollectionRequest" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestCollectionUri" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__7" | |
| } | |
| ], | |
| "description": "See help section for an explanation of dataset collections", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_type": "gx_data_collection", | |
| "title": "Select a paired collection" | |
| }, | |
| "iset_stats": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both \"250\" and \"250,25\" will work while \"250,,10\" will not. See below for details.", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Enter mean, standard deviation, max, and min for insert lengths." | |
| } | |
| }, | |
| "required": [ | |
| "fastq_input1" | |
| ], | |
| "title": "When_fastq_input_selector_paired_collection", | |
| "type": "object" | |
| }, | |
| "When_fastq_input_selector_paired_iv": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "fastq_input_selector": { | |
| "const": "paired_iv", | |
| "default": null, | |
| "title": "Fastq Input Selector", | |
| "type": "string" | |
| }, | |
| "fastq_input1": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__8" | |
| } | |
| ], | |
| "description": "Specify dataset with interleaved reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select fastq dataset" | |
| }, | |
| "iset_stats": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both \"250\" and \"250,25\" will work while \"250,,10\" will not. See below for details.", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Enter mean, standard deviation, max, and min for insert lengths." | |
| } | |
| }, | |
| "required": [ | |
| "fastq_input1" | |
| ], | |
| "title": "When_fastq_input_selector_paired_iv", | |
| "type": "object" | |
| }, | |
| "When_fastq_input_selector_single": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "fastq_input_selector": { | |
| "const": "single", | |
| "default": null, | |
| "title": "Fastq Input Selector", | |
| "type": "string" | |
| }, | |
| "fastq_input1": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__6" | |
| } | |
| ], | |
| "description": "Specify dataset with single reads", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Select fastq dataset" | |
| } | |
| }, | |
| "required": [ | |
| "fastq_input1" | |
| ], | |
| "title": "When_fastq_input_selector_single", | |
| "type": "object" | |
| }, | |
| "When_io_options_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": {}, | |
| "title": "When_io_options_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_io_options_selector_do_not_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "io_options_selector": { | |
| "const": "do_not_set", | |
| "default": null, | |
| "title": "Io Options Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_io_options_selector_do_not_set", | |
| "type": "object" | |
| }, | |
| "When_io_options_selector_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "io_options_selector": { | |
| "const": "set", | |
| "default": null, | |
| "title": "Io Options Selector", | |
| "type": "string" | |
| }, | |
| "five": { | |
| "default": null, | |
| "description": "Useful for HiC data", | |
| "gx_type": "gx_boolean", | |
| "title": "For split alignment, take alignment with smallest coordinate as primary", | |
| "type": "boolean" | |
| }, | |
| "q": { | |
| "default": null, | |
| "description": "By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score.", | |
| "gx_type": "gx_boolean", | |
| "title": "Don't lower MAPQ for split alignment", | |
| "type": "boolean" | |
| }, | |
| "T": { | |
| "default": null, | |
| "description": "-T; default=30", | |
| "gx_type": "gx_integer", | |
| "title": "Minimum score to output", | |
| "type": "integer" | |
| }, | |
| "h": { | |
| "default": null, | |
| "description": "-h; default=5", | |
| "gx_type": "gx_integer", | |
| "title": "If there are less than THIS VALUE hits with score >80% of the max score, output them all in the XA tag", | |
| "type": "integer" | |
| }, | |
| "a": { | |
| "default": null, | |
| "description": "-a; These alignments will be flagged as secondary alignments", | |
| "gx_type": "gx_boolean", | |
| "title": "Output all alignments for single-ends or unpaired paired-ends", | |
| "type": "boolean" | |
| }, | |
| "C": { | |
| "default": null, | |
| "description": "-C", | |
| "gx_type": "gx_boolean", | |
| "title": "Append FASTA/FASTQ comment to BAM output", | |
| "type": "boolean" | |
| }, | |
| "V": { | |
| "default": null, | |
| "description": "-C", | |
| "gx_type": "gx_boolean", | |
| "title": "Output the reference FASTA header in the XR tag", | |
| "type": "boolean" | |
| }, | |
| "Y": { | |
| "default": null, | |
| "description": "-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments", | |
| "gx_type": "gx_boolean", | |
| "title": "Use soft clipping for supplementary alignments", | |
| "type": "boolean" | |
| }, | |
| "M": { | |
| "default": null, | |
| "description": "-M; For Picard<1.96 compatibility", | |
| "gx_type": "gx_boolean", | |
| "title": "Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'", | |
| "type": "boolean" | |
| }, | |
| "K": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-K", | |
| "gx_type": "gx_integer", | |
| "title": "Process this number of input bases in each batch regardless of nThreads (for reproducibility)" | |
| } | |
| }, | |
| "title": "When_io_options_selector_set", | |
| "type": "object" | |
| }, | |
| "When_reference_source_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "ref_file": { | |
| "default": null, | |
| "description": "Select genome from the list", | |
| "gx_multiple": false, | |
| "gx_type": "gx_select", | |
| "title": "Using reference genome", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_reference_source_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_reference_source_selector_cached": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "reference_source_selector": { | |
| "const": "cached", | |
| "default": null, | |
| "title": "Reference Source Selector", | |
| "type": "string" | |
| }, | |
| "ref_file": { | |
| "default": null, | |
| "description": "Select genome from the list", | |
| "gx_multiple": false, | |
| "gx_type": "gx_select", | |
| "title": "Using reference genome", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_reference_source_selector_cached", | |
| "type": "object" | |
| }, | |
| "When_reference_source_selector_history": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "reference_source_selector": { | |
| "const": "history", | |
| "default": null, | |
| "title": "Reference Source Selector", | |
| "type": "string" | |
| }, | |
| "ref_file": { | |
| "anyOf": [ | |
| { | |
| "discriminator": { | |
| "mapping": { | |
| "hda": "#/$defs/DataRequestHda", | |
| "ld": "#/$defs/DataRequestLd", | |
| "ldda": "#/$defs/DataRequestLdda", | |
| "url": "#/$defs/DataRequestUri" | |
| }, | |
| "propertyName": "src" | |
| }, | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/DataRequestHda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLdda" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestLd" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestUri" | |
| } | |
| ] | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__1" | |
| } | |
| ], | |
| "description": "You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately.", | |
| "gx_extensions": [ | |
| "data" | |
| ], | |
| "gx_multiple": false, | |
| "gx_type": "gx_data", | |
| "title": "Use the following dataset as the reference" | |
| } | |
| }, | |
| "required": [ | |
| "ref_file" | |
| ], | |
| "title": "When_reference_source_selector_history", | |
| "type": "object" | |
| }, | |
| "When_rg_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": {}, | |
| "title": "When_rg_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_rg_selector_do_not_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "rg_selector": { | |
| "const": "do_not_set", | |
| "default": null, | |
| "title": "Rg Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_rg_selector_do_not_set", | |
| "type": "object" | |
| }, | |
| "When_rg_selector_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "rg_selector": { | |
| "const": "set", | |
| "default": null, | |
| "title": "Rg Selector", | |
| "type": "string" | |
| }, | |
| "read_group_id_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__4", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "read_group_sm_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__5", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "PL": { | |
| "anyOf": [ | |
| { | |
| "const": "CAPILLARY", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "LS454", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "ILLUMINA", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "SOLID", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "HELICOS", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "IONTORRENT", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "PACBIO", | |
| "type": "string" | |
| } | |
| ], | |
| "default": null, | |
| "gx_multiple": false, | |
| "gx_options": [ | |
| { | |
| "label": "CAPILLARY", | |
| "selected": false, | |
| "value": "CAPILLARY" | |
| }, | |
| { | |
| "label": "LS454", | |
| "selected": false, | |
| "value": "LS454" | |
| }, | |
| { | |
| "label": "ILLUMINA", | |
| "selected": true, | |
| "value": "ILLUMINA" | |
| }, | |
| { | |
| "label": "SOLID", | |
| "selected": false, | |
| "value": "SOLID" | |
| }, | |
| { | |
| "label": "HELICOS", | |
| "selected": false, | |
| "value": "HELICOS" | |
| }, | |
| { | |
| "label": "IONTORRENT", | |
| "selected": false, | |
| "value": "IONTORRENT" | |
| }, | |
| { | |
| "label": "PACBIO", | |
| "selected": false, | |
| "value": "PACBIO" | |
| } | |
| ], | |
| "gx_type": "gx_select", | |
| "title": "Platform/technology used to produce the reads (PL)" | |
| }, | |
| "read_group_lb_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__6", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "CN": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Sequencing center that produced the read (CN)" | |
| }, | |
| "DS": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Description (DS)" | |
| }, | |
| "DT": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "ISO8601 format date or date/time, like YYYY-MM-DD", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Date that run was produced (DT)" | |
| }, | |
| "FO": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\\*|[ACMGRSVTWYHKDBN]+/", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Flow order (FO)" | |
| }, | |
| "KS": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "The array of nucleotide bases that correspond to the key sequence of each read (KS)" | |
| }, | |
| "PG": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Programs used for processing the read group (PG)" | |
| }, | |
| "PI": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_type": "gx_integer", | |
| "title": "Predicted median insert size (PI)" | |
| }, | |
| "PU": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Platform unit (PU)" | |
| } | |
| }, | |
| "title": "When_rg_selector_set", | |
| "type": "object" | |
| }, | |
| "When_rg_selector_set_id_auto": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "rg_selector": { | |
| "const": "set_id_auto", | |
| "default": null, | |
| "title": "Rg Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_rg_selector_set_id_auto", | |
| "type": "object" | |
| }, | |
| "When_rg_selector_set_picard": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "rg_selector": { | |
| "const": "set_picard", | |
| "default": null, | |
| "title": "Rg Selector", | |
| "type": "string" | |
| }, | |
| "read_group_id_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__1", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "read_group_sm_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__2", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "read_group_lb_conditional": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__3", | |
| "default": null, | |
| "gx_test_help": "Use dataset name or collection information to automatically assign this value", | |
| "gx_test_label": "Auto-assign", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "PL": { | |
| "anyOf": [ | |
| { | |
| "const": "CAPILLARY", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "LS454", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "ILLUMINA", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "SOLID", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "HELICOS", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "IONTORRENT", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "PACBIO", | |
| "type": "string" | |
| } | |
| ], | |
| "default": null, | |
| "gx_multiple": false, | |
| "gx_options": [ | |
| { | |
| "label": "CAPILLARY", | |
| "selected": false, | |
| "value": "CAPILLARY" | |
| }, | |
| { | |
| "label": "LS454", | |
| "selected": false, | |
| "value": "LS454" | |
| }, | |
| { | |
| "label": "ILLUMINA", | |
| "selected": true, | |
| "value": "ILLUMINA" | |
| }, | |
| { | |
| "label": "SOLID", | |
| "selected": false, | |
| "value": "SOLID" | |
| }, | |
| { | |
| "label": "HELICOS", | |
| "selected": false, | |
| "value": "HELICOS" | |
| }, | |
| { | |
| "label": "IONTORRENT", | |
| "selected": false, | |
| "value": "IONTORRENT" | |
| }, | |
| { | |
| "label": "PACBIO", | |
| "selected": false, | |
| "value": "PACBIO" | |
| } | |
| ], | |
| "gx_type": "gx_select", | |
| "title": "Platform/technology used to produce the reads (PL)" | |
| }, | |
| "PU": { | |
| "default": null, | |
| "description": "Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Platform unit (PU)", | |
| "type": "string" | |
| }, | |
| "CN": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Sequencing center that produced the read (CN)" | |
| }, | |
| "DS": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Description (DS)" | |
| }, | |
| "PI": { | |
| "anyOf": [ | |
| { | |
| "type": "integer" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_type": "gx_integer", | |
| "title": "Predicted median insert size (PI)" | |
| }, | |
| "DT": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "ISO8601 format date or date/time, like YYYY-MM-DD", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Date that run was produced (DT)" | |
| } | |
| }, | |
| "title": "When_rg_selector_set_picard", | |
| "type": "object" | |
| }, | |
| "When_scoring_options_selector___absent": { | |
| "additionalProperties": false, | |
| "properties": {}, | |
| "title": "When_scoring_options_selector___absent", | |
| "type": "object" | |
| }, | |
| "When_scoring_options_selector_do_not_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "scoring_options_selector": { | |
| "const": "do_not_set", | |
| "default": null, | |
| "title": "Scoring Options Selector", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_scoring_options_selector_do_not_set", | |
| "type": "object" | |
| }, | |
| "When_scoring_options_selector_set": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "scoring_options_selector": { | |
| "const": "set", | |
| "default": null, | |
| "title": "Scoring Options Selector", | |
| "type": "string" | |
| }, | |
| "A": { | |
| "default": null, | |
| "description": "-A; scales options -T, -d, -B, -O, -E, -L, and -U unless overridden; default=1", | |
| "gx_type": "gx_integer", | |
| "title": "Score for a sequence match", | |
| "type": "integer" | |
| }, | |
| "B": { | |
| "default": null, | |
| "description": "-B; default=4", | |
| "gx_type": "gx_integer", | |
| "title": "Penalty for a mismatch", | |
| "type": "integer" | |
| }, | |
| "O": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-O; default=6,6", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Gap open penalties for deletions and insertions" | |
| }, | |
| "E": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-E; default=1,1", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Gap extension penalties; a gap of size k cost '-O + -E*k'. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" | |
| }, | |
| "L": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "-L; default=5,5; When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Penalties for 5'-end and 3'-end clipping" | |
| }, | |
| "U": { | |
| "default": null, | |
| "description": "-U; default=17", | |
| "gx_type": "gx_integer", | |
| "title": "Penalty for an unpaired read pair", | |
| "type": "integer" | |
| } | |
| }, | |
| "title": "When_scoring_options_selector_set", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__1": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__1" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__1" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__10": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_reference_source_selector_cached" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_reference_source_selector___absent" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_reference_source_selector_history" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__11": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_fastq_input_selector_paired" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_fastq_input_selector___absent" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_fastq_input_selector_single" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_fastq_input_selector_paired_collection" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_fastq_input_selector_paired_iv" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__12": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_rg_selector_set_picard" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_rg_selector_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_rg_selector_set_id_auto" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_rg_selector_do_not_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_rg_selector___absent" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__13": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector_illumina" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector___absent" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector_pacbio" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector_ont2d" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector_intractg" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_analysis_type_selector_full" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__2": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__2" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__2" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__3": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__3" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__3" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__4": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__4" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__4" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__5": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__5" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__5" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__6": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_do_auto_name_True" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name_False__6" | |
| }, | |
| { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__When_do_auto_name___absent__6" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__7": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_algorithmic_options_selector_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_algorithmic_options_selector_do_not_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_algorithmic_options_selector___absent" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__8": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_scoring_options_selector_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_scoring_options_selector_do_not_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_scoring_options_selector___absent" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__9": { | |
| "oneOf": [ | |
| { | |
| "$ref": "#/$defs/When_io_options_selector_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_io_options_selector_do_not_set" | |
| }, | |
| { | |
| "$ref": "#/$defs/When_io_options_selector___absent" | |
| } | |
| ], | |
| "title": "ConditionalType" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__1": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "ID": { | |
| "default": null, | |
| "description": "This value must be unique among multiple samples in your experiment", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group identifier (ID)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__2": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "SM": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "This value should be descriptive. Use pool name where a pool is being sequenced", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group sample name (SM)" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__3": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "LB": { | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Library name (LB)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__4": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "ID": { | |
| "default": null, | |
| "description": "This value must be unique among multiple samples in your experiment", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group identifier (ID)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__5": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "SM": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "This value should be descriptive. Use pool name where a pool is being sequenced", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group sample name (SM)" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name_False__6": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "do_auto_name": { | |
| "const": false, | |
| "default": null, | |
| "title": "Do Auto Name", | |
| "type": "boolean" | |
| }, | |
| "LB": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Library name (LB)" | |
| } | |
| }, | |
| "title": "When_do_auto_name_False", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__1": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "ID": { | |
| "default": null, | |
| "description": "This value must be unique among multiple samples in your experiment", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group identifier (ID)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__2": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "SM": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "This value should be descriptive. Use pool name where a pool is being sequenced", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group sample name (SM)" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__3": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "LB": { | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Library name (LB)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__4": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "ID": { | |
| "default": null, | |
| "description": "This value must be unique among multiple samples in your experiment", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group identifier (ID)", | |
| "type": "string" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__5": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "SM": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "description": "This value should be descriptive. Use pool name where a pool is being sequenced", | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Read group sample name (SM)" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__When_do_auto_name___absent__6": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "LB": { | |
| "anyOf": [ | |
| { | |
| "type": "string" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "gx_area": false, | |
| "gx_type": "gx_text", | |
| "title": "Library name (LB)" | |
| } | |
| }, | |
| "title": "When_do_auto_name___absent", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__1": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__2": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__3": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__4": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__5": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__6": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__7": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "anyOf": [ | |
| { | |
| "$ref": "#/$defs/DataCollectionRequest" | |
| }, | |
| { | |
| "$ref": "#/$defs/DataRequestCollectionUri" | |
| } | |
| ] | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| }, | |
| "galaxy__tool_util_models__parameters__allow_batching___locals___BatchRequest__8": { | |
| "additionalProperties": false, | |
| "properties": { | |
| "__class__": { | |
| "const": "Batch", | |
| "title": "Class", | |
| "type": "string" | |
| }, | |
| "values": { | |
| "items": { | |
| "$ref": "#/$defs/BatchDataInstance" | |
| }, | |
| "title": "Values", | |
| "type": "array" | |
| }, | |
| "linked": { | |
| "anyOf": [ | |
| { | |
| "type": "boolean" | |
| }, | |
| { | |
| "type": "null" | |
| } | |
| ], | |
| "default": null, | |
| "title": "Linked" | |
| } | |
| }, | |
| "required": [ | |
| "__class__", | |
| "values" | |
| ], | |
| "title": "BatchRequest", | |
| "type": "object" | |
| } | |
| }, | |
| "additionalProperties": false, | |
| "properties": { | |
| "reference_source": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__10", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Use a built-in genome index", | |
| "selected": false, | |
| "value": "cached" | |
| }, | |
| { | |
| "label": "Use a reference from history and build index if necessary", | |
| "selected": false, | |
| "value": "history" | |
| } | |
| ], | |
| "gx_test_help": "Built-ins were indexed using default options. See `Indexes` section of help below", | |
| "gx_test_label": "Will you select a reference genome from your history or use a built-in index?", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "fastq_input": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__11", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Paired", | |
| "selected": false, | |
| "value": "paired" | |
| }, | |
| { | |
| "label": "Single", | |
| "selected": false, | |
| "value": "single" | |
| }, | |
| { | |
| "label": "Paired Collection", | |
| "selected": false, | |
| "value": "paired_collection" | |
| }, | |
| { | |
| "label": "Paired Interleaved", | |
| "selected": false, | |
| "value": "paired_iv" | |
| } | |
| ], | |
| "gx_test_help": "Select between paired and single end data", | |
| "gx_test_label": "Single or Paired-end reads", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "rg": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__12", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "Set read groups (SAM/BAM specification)", | |
| "selected": false, | |
| "value": "set" | |
| }, | |
| { | |
| "label": "Set read groups (Picard style)", | |
| "selected": false, | |
| "value": "set_picard" | |
| }, | |
| { | |
| "label": "Automatically assign ID", | |
| "selected": false, | |
| "value": "set_id_auto" | |
| }, | |
| { | |
| "label": "Do not set", | |
| "selected": true, | |
| "value": "do_not_set" | |
| } | |
| ], | |
| "gx_test_help": "Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.", | |
| "gx_test_label": "Set read groups information?", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "analysis_type": { | |
| "$ref": "#/$defs/galaxy__tool_util_models__parameters__ConditionalParameterModel__pydantic_template___locals___ConditionalType__13", | |
| "default": null, | |
| "gx_options": [ | |
| { | |
| "label": "1.Simple Illumina mode", | |
| "selected": false, | |
| "value": "illumina" | |
| }, | |
| { | |
| "label": "2.PacBio mode (-x pacbio)", | |
| "selected": false, | |
| "value": "pacbio" | |
| }, | |
| { | |
| "label": "3.Nanopore 2D-reads mode (-x ont2d)", | |
| "selected": false, | |
| "value": "ont2d" | |
| }, | |
| { | |
| "label": "4.Intra-species contigs mode (-x intractg)", | |
| "selected": false, | |
| "value": "intractg" | |
| }, | |
| { | |
| "label": "5.Full list of options", | |
| "selected": false, | |
| "value": "full" | |
| } | |
| ], | |
| "gx_test_label": "Select analysis mode", | |
| "gx_type": "gx_conditional" | |
| }, | |
| "output_sort": { | |
| "anyOf": [ | |
| { | |
| "const": "coordinate", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "name", | |
| "type": "string" | |
| }, | |
| { | |
| "const": "unsorted", | |
| "type": "string" | |
| } | |
| ], | |
| "default": null, | |
| "description": "The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).", | |
| "gx_multiple": false, | |
| "gx_options": [ | |
| { | |
| "label": "Sort by chromosomal coordinates", | |
| "selected": true, | |
| "value": "coordinate" | |
| }, | |
| { | |
| "label": "Sort by read names (i.e., the QNAME field) ", | |
| "selected": false, | |
| "value": "name" | |
| }, | |
| { | |
| "label": "Not sorted (sorted as input)", | |
| "selected": false, | |
| "value": "unsorted" | |
| } | |
| ], | |
| "gx_type": "gx_select", | |
| "title": "BAM sorting mode" | |
| } | |
| }, | |
| "title": "DynamicModelForTool", | |
| "type": "object", | |
| "$schema": "https://json-schema.org/draft/2020-12/schema" | |
| } |
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