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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/apostl commit 79aa418c07e54b5f152681452767f7c8a40379b6 |
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added:
Galaxy-Workflow-APOSTL_Workflow.ga repository_dependencies.xml |
| b |
| diff -r 000000000000 -r 0b6e9cc279fc Galaxy-Workflow-APOSTL_Workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-APOSTL_Workflow.ga Thu May 11 14:52:17 2017 -0400 |
| [ |
| b'@@ -0,0 +1,1477 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "APOSTL Workflow", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Protein Database Downloader", \n+ "outputs": [\n+ {\n+ "name": "output_database", \n+ "type": "fasta"\n+ }\n+ ], \n+ "position": {\n+ "left": 119, \n+ "top": 428\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionoutput_database": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \n+ "output_name": "output_database"\n+ }, \n+ "RenameDatasetActionoutput_database": {\n+ "action_arguments": {\n+ "newname": "Human SwissProt dB April 12, 2017"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output_database"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", \n+ "tool_shed_repository": {\n+ "changeset_revision": "19ee2e85931a", \n+ "name": "dbbuilder", \n+ "owner": "galaxyp", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"source\\": \\"{\\\\\\"url\\\\\\": \\\\\\"https://raw.githubusercontent.com/pravs3683/databases/master/uniprot_swissprot_12April2017.fasta\\\\\\", \\\\\\"from\\\\\\": \\\\\\"url\\\\\\", \\\\\\"__current_case__\\\\\\": 2}\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n+ "tool_version": "0.2.1", \n+ "type": "tool", \n+ "uuid": "799e95bc-23e4-4c7b-b182-83c321892d42", \n+ "workflow_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Protein Database Downloader", \n+ "outputs": [\n+ {\n+ "name": "output_database", \n+ "type": "fasta"\n+ }\n+ ], \n+ "position": {\n+ "left": 124, \n+ "top": 532\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutput_database": {\n+ "action_arguments": {\n+ "newname": "cRAP dB (common Repository of Adventitious Proteins database)"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output_database"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.2.1", \n+ "tool_shed_repository": {\n+ "changeset_revision": "19ee2e85931a", \n+ "name": "dbbuilder", \n+ "owner": "galaxyp", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"source\\": \\"{\\\\\\"from\\\\\\": \\\\\\"cRAP\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"__rerun_remap_job_id__\\": null, \\"__page__\\": 0}", \n+ "tool_version": "0.2.1", \n+ "type": "tool", \n+ "uuid": "2f17233d-f5aa-4f18-85ed-d6568fafb0e5", \n+ "workflow_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 2, \n+ '..b'"tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"fasta_db\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"species\\": \\"\\\\\\"HUMAN\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "uuid": "16096e29-d534-4a6d-9627-e7e287798c71", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "CrapomeFile", \n+ "uuid": "1f90a8ba-22ee-45c4-9018-98a153162583"\n+ }\n+ ]\n+ }, \n+ "18": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", \n+ "id": 18, \n+ "input_connections": {\n+ "bait_input": {\n+ "id": 16, \n+ "output_name": "Bait_file"\n+ }, \n+ "inter_input": {\n+ "id": 16, \n+ "output_name": "Inter_file"\n+ }, \n+ "prey_input": {\n+ "id": 16, \n+ "output_name": "Prey_file"\n+ }\n+ }, \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool SAINTexpress", \n+ "name": "go_file"\n+ }, \n+ {\n+ "description": "runtime parameter for tool SAINTexpress", \n+ "name": "bait_input"\n+ }, \n+ {\n+ "description": "runtime parameter for tool SAINTexpress", \n+ "name": "inter_input"\n+ }, \n+ {\n+ "description": "runtime parameter for tool SAINTexpress", \n+ "name": "prey_input"\n+ }\n+ ], \n+ "label": null, \n+ "name": "SAINTexpress", \n+ "outputs": [\n+ {\n+ "name": "SAINT_output", \n+ "type": "txt"\n+ }\n+ ], \n+ "position": {\n+ "left": 1763.5, \n+ "top": 524\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionSAINT_output": {\n+ "action_arguments": {\n+ "newname": "SAINT Output File"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "SAINT_output"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/bornea/saintexpress/saint_wrapper/1.0.0", \n+ "tool_shed_repository": {\n+ "changeset_revision": "67631a640534", \n+ "name": "saintexpress", \n+ "owner": "bornea", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"rep_num\\": \\"\\\\\\"100\\\\\\"\\", \\"__page__\\": 0, \\"go_file\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__rerun_remap_job_id__\\": null, \\"bait_input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"vc_bool\\": \\"\\\\\\"false\\\\\\"\\", \\"inter_input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"go_bool\\": \\"\\\\\\"false\\\\\\"\\", \\"prey_input\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"vc_num\\": \\"\\\\\\"1\\\\\\"\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "uuid": "86e2c9ce-be72-496b-84c2-7e3027d0187e", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "SAINT_output", \n+ "uuid": "f4c612f6-d132-444f-9474-f95f7b968382"\n+ }\n+ ]\n+ }\n+ }, \n+ "uuid": "4f118197-8eee-42d5-ba46-3abfcb3f127b"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 0b6e9cc279fc repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu May 11 14:52:17 2017 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<repositories description="This workflow requires a number of different repositories."> + <repository changeset_revision="f1459638e1bc" name="query_crapome" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="6ad498eac0e2" name="saint_preprocessing" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="67631a640534" name="saintexpress" owner="bornea" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="19ee2e85931a" name="dbbuilder" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="2904d46167da" name="fasta_merge_files_and_filter_unique_sequences" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7f2aeb19650f" name="peptideshaker" owner="galaxyp" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |