# HG changeset patch # User galaxyp # Date 1489668323 14400 # Node ID 338a6d72477480eea956aeb6932c3c9846a1d89d # Parent eb71034189fb5fb1181585b09e896a2fcbb70952 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/abrf2017_workshop commit e81bd1614788b8bfe8752c4a4279abdcc34e9777 diff -r eb71034189fb -r 338a6d724774 Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-ABRF_UNIPEPT__Peptide_GO_Summary_Step2.ga Thu Mar 16 08:45:23 2017 -0400 @@ -0,0 +1,350 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "ABRF UNIPEPT: Peptide GO Summary Step2", + "steps": { + "0": { + "annotation": "", + "content_id": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Gene Ontology Terms" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 193, + "top": 231.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Gene Ontology Terms\"}", + "tool_version": null, + "type": "data_input", + "uuid": "60bd46b9-2911-4a36-94ac-e51e66a9a6e2", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "7a0ce548-f4a1-4cf9-8e0c-2cc4092eb6cd" + } + ] + }, + "1": { + "annotation": "", + "content_id": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Sample 1 Pept2Prot (extra fields) Normalized" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 195, + "top": 310.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Sample 1 Pept2Prot (extra fields) Normalized\"}", + "tool_version": null, + "type": "data_input", + "uuid": "52b44ffd-15ff-421b-977a-6b9a512d1582", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "5d5337c5-f228-4054-92cf-f3e800f2a666" + } + ] + }, + "2": { + "annotation": "", + "content_id": null, + "id": 2, + "input_connections": {}, + "inputs": [ + { + "description": "", + "name": "Sample 1 PSM Report" + } + ], + "label": null, + "name": "Input dataset", + "outputs": [], + "position": { + "left": 197, + "top": 386.5 + }, + "tool_errors": null, + "tool_id": null, + "tool_state": "{\"name\": \"Sample 1 PSM Report\"}", + "tool_version": null, + "type": "data_input", + "uuid": "2c906b80-b425-4280-9743-4151b15fd3f4", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "ba24d136-484f-49c8-964f-982b56b26217" + } + ] + }, + "3": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", + "id": 3, + "input_connections": { + "tables_0|table": { + "id": 0, + "output_name": "output" + }, + "tables_1|table": { + "id": 1, + "output_name": "output" + }, + "tables_2|table": { + "id": 2, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Query Tabular", + "name": "add_to_database" + } + ], + "label": null, + "name": "Query Tabular", + "outputs": [ + { + "name": "sqlitedb", + "type": "sqlite" + }, + { + "name": "output", + "type": "tabular" + } + ], + "position": { + "left": 442, + "top": 230 + }, + "post_job_actions": { + "RenameDatasetActionoutput": { + "action_arguments": { + "newname": "Bering Strait BIOLOGICAL PROCESS" + }, + "action_type": "RenameDatasetAction", + "output_name": "output" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/2.0.0", + "tool_shed_repository": { + "changeset_revision": "e84d1c3bf4fe", + "name": "query_tabular", + "owner": "jjohnson", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"tables\": \"[{\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"go\\\", \\\"col_names\\\": \\\"aspect,go_id,description\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_id\\\"}, {\\\"__index__\\\": 1, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"aspect,go_id,description\\\"}]}, \\\"__index__\\\": 0, \\\"input_opts\\\": {\\\"linefilters\\\": []}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"false\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering\\\", \\\"col_names\\\": \\\"peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_reference,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids\\\", \\\"indexes\\\": [{\\\"__index__\\\": 0, \\\"unique\\\": \\\"false\\\", \\\"index_columns\\\": \\\"go_reference,peptide\\\"}]}, \\\"__index__\\\": 1, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"comment_char\\\": \\\"#\\\", \\\"__current_case__\\\": 1, \\\"filter_type\\\": \\\"comment\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, {\\\"tbl_opts\\\": {\\\"load_named_columns\\\": \\\"true\\\", \\\"pkey_autoincr\\\": \\\"\\\", \\\"table_name\\\": \\\"bering_psms\\\", \\\"col_names\\\": \\\"id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation\\\", \\\"indexes\\\": []}, \\\"__index__\\\": 2, \\\"input_opts\\\": {\\\"linefilters\\\": [{\\\"filter\\\": {\\\"regex_action\\\": \\\"include_match\\\", \\\"regex_pattern\\\": \\\"^\\\\\\\\d\\\", \\\"__current_case__\\\": 2, \\\"filter_type\\\": \\\"regex\\\"}, \\\"__index__\\\": 0}]}, \\\"table\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"save_db\": \"\\\"true\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\", \"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\"\\\\n FROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'biological_process'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"add_to_database\": \"{\\\"withdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"workdb\": \"\\\"workdb.sqlite\\\"\"}", + "tool_version": "2.0.0", + "type": "tool", + "uuid": "8f335601-0ed2-4da1-8d51-3ad443f71400", + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e662208f-4587-4b09-9e15-ccc7abb7268a" + }, + { + "label": null, + "output_name": "sqlitedb", + "uuid": "4b685349-25cb-4459-9950-6207b94bafe6" + } + ] + }, + "4": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "id": 4, + "input_connections": { + "sqlitedb": { + "id": 3, + "output_name": "sqlitedb" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SQLite to tabular", + "name": "sqlitedb" + } + ], + "label": null, + "name": "SQLite to tabular", + "outputs": [ + { + "name": "query_results", + "type": "tabular" + } + ], + "position": { + "left": 874, + "top": 204 + }, + "post_job_actions": { + "RenameDatasetActionquery_results": { + "action_arguments": { + "newname": "Bering Strait MOLECULAR FUNCTION" + }, + "action_type": "RenameDatasetAction", + "output_name": "query_results" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "tool_shed_repository": { + "changeset_revision": "123b9ca5e26a", + "name": "sqlite_to_tabular", + "owner": "jjohnson", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'molecular_function'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "ff3593c9-a8eb-4b26-858d-e156de462541", + "workflow_outputs": [ + { + "label": null, + "output_name": "query_results", + "uuid": "4fd55eff-0f1e-47f2-b4aa-da2ebc91bcda" + } + ] + }, + "5": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "id": 5, + "input_connections": { + "sqlitedb": { + "id": 3, + "output_name": "sqlitedb" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SQLite to tabular", + "name": "sqlitedb" + } + ], + "label": null, + "name": "SQLite to tabular", + "outputs": [ + { + "name": "query_results", + "type": "tabular" + } + ], + "position": { + "left": 876, + "top": 342 + }, + "post_job_actions": { + "RenameDatasetActionquery_results": { + "action_arguments": { + "newname": "Bering Strait CELLULAR COMPONENT" + }, + "action_type": "RenameDatasetAction", + "output_name": "query_results" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "tool_shed_repository": { + "changeset_revision": "123b9ca5e26a", + "name": "sqlite_to_tabular", + "owner": "jjohnson", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"sqlquery\": \"\\\"SELECT g.description, count(distinct b.peptide) as \\\\\\\"bering_peptides\\\\\\\", count(distinct b.id) as \\\\\\\"bering_psms\\\\\\\" \\\\nFROM go as g JOIN\\\\n ( SELECT go.description, bering.peptide, bering_psms.id\\\\n FROM go LEFT OUTER JOIN bering ON go.go_id = bering.go_reference JOIN bering_psms ON bering.peptide = bering_psms.sequence\\\\n GROUP BY go.description, bering.peptide, bering_psms.id\\\\n ) as b ON g.description = b.description \\\\nWHERE g.aspect = 'cellular_component'\\\\nGROUP BY g.description\\\\nORDER BY bering_peptides desc,bering_psms desc\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "4aadf296-0c45-43bb-a146-e267c2955233", + "workflow_outputs": [ + { + "label": null, + "output_name": "query_results", + "uuid": "6042e237-57f6-489e-b8a7-5d32afd39d5e" + } + ] + }, + "6": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "id": 6, + "input_connections": { + "sqlitedb": { + "id": 3, + "output_name": "sqlitedb" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool SQLite to tabular", + "name": "sqlitedb" + } + ], + "label": null, + "name": "SQLite to tabular", + "outputs": [ + { + "name": "query_results", + "type": "tabular" + } + ], + "position": { + "left": 882, + "top": 458.5 + }, + "post_job_actions": { + "RenameDatasetActionquery_results": { + "action_arguments": { + "newname": "Bering Strait PEPTIDES and PSMs" + }, + "action_type": "RenameDatasetAction", + "output_name": "query_results" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1", + "tool_shed_repository": { + "changeset_revision": "123b9ca5e26a", + "name": "sqlite_to_tabular", + "owner": "jjohnson", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"sqlquery\": \"\\\"SELECT sequence as \\\\\\\"peptide\\\\\\\", count(id) as \\\\\\\"PSMs\\\\\\\"\\\\nFROM bering_psms\\\\nWHERE validation IS NOT 'Confident' AND confidence >= 95\\\\nGROUP BY sequence\\\\nORDER BY sequence\\\\n\\\"\", \"__page__\": 0, \"sqlitedb\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"no_header\": \"\\\"false\\\"\"}", + "tool_version": "0.0.1", + "type": "tool", + "uuid": "e172020f-dd58-4027-9d6c-94273ec2aee8", + "workflow_outputs": [ + { + "label": null, + "output_name": "query_results", + "uuid": "291d94c5-9ff7-44ae-872f-76955c56d6f4" + } + ] + } + }, + "uuid": "57999e7e-0de6-41e0-87d3-1660414d9896" +} \ No newline at end of file