| Previous changeset 7:0b7210ad9187 (2016-06-25) |
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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty |
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modified:
amrplusplus_workflow.ga repository_dependencies.xml |
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| diff -r 0b7210ad9187 -r 0eae27b15aa0 amrplusplus_workflow.ga --- a/amrplusplus_workflow.ga Sat Jun 25 17:17:42 2016 -0400 +++ b/amrplusplus_workflow.ga Thu Jul 14 19:04:32 2016 -0400 |
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| b'@@ -2,7 +2,7 @@\n "a_galaxy_workflow": "true", \n "annotation": "", \n "format-version": "0.1", \n- "name": "amrplusplus workflow", \n+ "name": "amrplusplus workflow (imported from uploaded file)", \n "steps": {\n "0": {\n "annotation": "", \n@@ -237,8 +237,61 @@\n }, \n "5": {\n "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0", \n+ "id": 5, \n+ "input_connections": {\n+ "reference": {\n+ "id": 3, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool MetaSNP", \n+ "name": "sam_type"\n+ }, \n+ {\n+ "description": "runtime parameter for tool MetaSNP", \n+ "name": "reference"\n+ }\n+ ], \n+ "label": null, \n+ "name": "MetaSNP", \n+ "outputs": [\n+ {\n+ "name": "output", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 1447, \n+ "top": 543\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0", \n+ "tool_shed_repository": {\n+ "changeset_revision": "a3d1f2a85806", \n+ "name": "metasnp", \n+ "owner": "chrisd", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"sam_type\\": \\"{\\\\\\"best\\\\\\": \\\\\\"false\\\\\\", \\\\\\"sampe_input\\\\\\": {\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}, \\\\\\"mode\\\\\\": \\\\\\"paired_end\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"reference\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_version": "0.1.0", \n+ "type": "tool", \n+ "uuid": "f126b5ac-a201-4478-8336-cdc6d70c54ca", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output", \n+ "uuid": "2a7f2c96-ce1d-4ce0-b8cb-ba31df13bdb6"\n+ }\n+ ]\n+ }, \n+ "6": {\n+ "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", \n- "id": 5, \n+ "id": 6, \n "input_connections": {\n "input_type|fastq_input1": {\n "id": 4, \n@@ -300,13 +353,13 @@\n }\n ]\n }, \n- "6": {\n+ "7": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1", \n- "id": 6, \n+ "id": 7, \n "input_connections": {\n "input": {\n- "id": 5, \n+ "id": 6, \n "output_name": "bam_output"\n }\n }, \n@@ -349,13 +402,13 @@\n }\n ]\n }, \n- "7": {\n+ "8": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1", \n- "id": 7, \n+ "id": 8, \n "input_connections": {\n "input_type|bam_input": {\n- "id": 6, \n+ "id": 7, \n "output_name": "output"\n }, \n "reference_source|ref_file": {\n@@ -406,13 +459,13 @@\n }\n ]\n }, \n- "8": {\n+ "9": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0", \n- "'..b'\\"}}\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n- "tool_version": "0.1.0", \n- "type": "tool", \n- "uuid": "3c0b1793-8625-4529-a406-6ffa822b38ab", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output1", \n- "uuid": "b58e3331-4b37-49d9-b311-1120ca9606e6"\n- }\n- ]\n- }, \n "11": {\n "annotation": "", \n "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n "id": 11, \n "input_connections": {\n- "input1": {\n+ "reference": {\n "id": 3, \n "output_name": "output"\n }, \n- "input2": {\n- "id": 9, \n+ "sam": {\n+ "id": 10, \n "output_name": "output1"\n }\n }, \n "inputs": [\n {\n "description": "runtime parameter for tool Coverage Sampler", \n- "name": "input2"\n+ "name": "reference"\n }, \n {\n "description": "runtime parameter for tool Coverage Sampler", \n- "name": "input1"\n+ "name": "sam"\n }\n ], \n "label": null, \n "name": "Coverage Sampler", \n "outputs": [\n {\n- "name": "output1", \n+ "name": "output", \n "type": "tabular"\n }\n ], \n "position": {\n- "left": 1618.5, \n- "top": 553\n+ "left": 1631.5, \n+ "top": 545\n }, \n- "post_job_actions": {\n- "HideDatasetActionoutput1": {\n- "action_arguments": {}, \n- "action_type": "HideDatasetAction", \n- "output_name": "output1"\n- }\n- }, \n+ "post_job_actions": {}, \n "tool_errors": null, \n "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n "tool_shed_repository": {\n- "changeset_revision": "72901052a829", \n+ "changeset_revision": "ec439b0e7512", \n "name": "coverage_sampler", \n "owner": "chrisd", \n "tool_shed": "toolshed.g2.bx.psu.edu"\n }, \n- "tool_state": "{\\"input2\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__page__\\": 0, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"min\\": \\"\\\\\\"5\\\\\\"\\", \\"max\\": \\"\\\\\\"100\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"samples\\": \\"\\\\\\"1\\\\\\"\\", \\"skip\\": \\"\\\\\\"5\\\\\\"\\", \\"threshold\\": \\"\\\\\\"80\\\\\\"\\"}", \n+ "tool_state": "{\\"__page__\\": 0, \\"reference\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"sam\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"min\\": \\"\\\\\\"5\\\\\\"\\", \\"max\\": \\"\\\\\\"100\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"samples\\": \\"\\\\\\"1\\\\\\"\\", \\"skip\\": \\"\\\\\\"5\\\\\\"\\", \\"threshold\\": \\"\\\\\\"80\\\\\\"\\"}", \n "tool_version": "0.1.0", \n "type": "tool", \n- "uuid": "0907193f-3458-40a1-b0ba-beac3998da62", \n- "workflow_outputs": []\n+ "uuid": "a74c17eb-f115-40b3-847d-03b89c251bc7", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output", \n+ "uuid": "57902fb4-a733-4429-8dfd-905ad0dd2f03"\n+ }\n+ ]\n }\n }, \n- "uuid": "5f790d55-b08b-45e8-8471-005678ec4eef"\n+ "uuid": "9ed4d064-e299-406d-a56f-e7eec8120829"\n }\n\\ No newline at end of file\n' |
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| diff -r 0b7210ad9187 -r 0eae27b15aa0 repository_dependencies.xml --- a/repository_dependencies.xml Sat Jun 25 17:17:42 2016 -0400 +++ b/repository_dependencies.xml Thu Jul 14 19:04:32 2016 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="A meta-package of tools needed to run the amrPlusPlus workflow"> - <repository changeset_revision="29818e0c3fb5" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="284f6d4422a6" name="suite_amrplusplus" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |