| Previous changeset 0:834c10340bce (2016-03-23) Next changeset 2:7550d3bc44a4 (2016-03-24) |
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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 159373642da0dd9e011280de5515b020189dd521 |
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modified:
repository_dependencies.xml |
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added:
amrplusplus_wf.ga |
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removed:
Galaxy-Workflow-AmrPlusPlus_PE.ga |
| b |
| diff -r 834c10340bce -r 11cb57237849 Galaxy-Workflow-AmrPlusPlus_PE.ga --- a/Galaxy-Workflow-AmrPlusPlus_PE.ga Wed Mar 23 21:49:48 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,559 +0,0 @@\n-{\n- "a_galaxy_workflow": "true", \n- "annotation": "", \n- "format-version": "0.1", \n- "name": "AmrPlusPlus_PE", \n- "steps": {\n- "0": {\n- "annotation": "The genome to align non-host reads to", \n- "content_id": null, \n- "id": 0, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "The genome to align non-host reads to", \n- "name": "AMR Database"\n- }\n- ], \n- "label": "AMR Database", \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 391, \n- "top": 200\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"AMR Database\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "uuid": "66a5eb48-4b35-46cc-9b93-fd88d97d2218", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output", \n- "uuid": "d30b93c8-aa9f-49eb-801f-5a02e68a876b"\n- }\n- ]\n- }, \n- "1": {\n- "annotation": "Genome used to filter reads on", \n- "content_id": null, \n- "id": 1, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "Genome used to filter reads on", \n- "name": "Host Genome"\n- }\n- ], \n- "label": "Host Genome", \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 391, \n- "top": 285\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"Host Genome\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "uuid": "02603c1f-b5f0-4121-9b57-005a98411364", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output", \n- "uuid": "6b4607b2-f4d8-4b24-ade6-30b2a6377017"\n- }\n- ]\n- }, \n- "2": {\n- "annotation": "Forward reads", \n- "content_id": null, \n- "id": 2, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "Forward reads", \n- "name": "FastQ Forward"\n- }\n- ], \n- "label": "FastQ Forward", \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 391, \n- "top": 370\n- }, \n- "tool_errors": null, \n- "tool_id": null, \n- "tool_state": "{\\"name\\": \\"FastQ Forward\\"}", \n- "tool_version": null, \n- "type": "data_input", \n- "uuid": "f25b69be-a40e-4d89-8535-84e2c3784148", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output", \n- "uuid": "cd11b688-012e-4d6e-bac7-a35c97057e8e"\n- }\n- ]\n- }, \n- "3": {\n- "annotation": "Reverse reads", \n- "content_id": null, \n- "id": 3, \n- "input_connections": {}, \n- "inputs": [\n- {\n- "description": "Reverse reads", \n- "name": "FastQ Reverse"\n- }\n- ], \n- "label": "FastQ Reverse", \n- "name": "Input dataset", \n- "outputs": [], \n- "position": {\n- "left": 391, \n- "top": 455\n- }, \n- "tool_errors": null, \n- '..b'annotation": "", \n- "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", \n- "id": 10, \n- "input_connections": {\n- "input1": {\n- "id": 0, \n- "output_name": "output"\n- }, \n- "sam_type|sampe_input2": {\n- "id": 9, \n- "output_name": "output1"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "Snip Finder", \n- "outputs": [\n- {\n- "name": "output1", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 2501, \n- "top": 200\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutput1": {\n- "action_arguments": {\n- "newname": "Snip Results"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "output1"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", \n- "tool_state": "{\\"sam_type\\": \\"{\\\\\\"best\\\\\\": \\\\\\"False\\\\\\", \\\\\\"mode\\\\\\": \\\\\\"paired_end\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"sampe_input2\\\\\\": null}\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\"}", \n- "tool_version": "0.1.0", \n- "type": "tool", \n- "uuid": "197e5f9d-b4e5-449b-9b2d-67c939f34e32", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output1", \n- "uuid": "768cb726-399b-490e-82c1-8d523f7208ee"\n- }\n- ]\n- }, \n- "11": {\n- "annotation": "", \n- "content_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n- "id": 11, \n- "input_connections": {\n- "input1": {\n- "id": 0, \n- "output_name": "output"\n- }, \n- "input2": {\n- "id": 9, \n- "output_name": "output1"\n- }\n- }, \n- "inputs": [], \n- "label": null, \n- "name": "Coverage Sampler", \n- "outputs": [\n- {\n- "name": "output1", \n- "type": "tabular"\n- }\n- ], \n- "position": {\n- "left": 2501, \n- "top": 341\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutput1": {\n- "action_arguments": {\n- "newname": "Coverage Results"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "output1"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "testtoolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n- "tool_state": "{\\"input2\\": \\"null\\", \\"__page__\\": 0, \\"input1\\": \\"null\\", \\"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": "8ffc98a9-82b8-429c-bd1d-fa4f24b22148", \n- "workflow_outputs": [\n- {\n- "label": null, \n- "output_name": "output1", \n- "uuid": "207d0359-f140-47bb-9e2c-4882e2697e82"\n- }\n- ]\n- }\n- }, \n- "uuid": "c3b33138-479d-4709-9a3a-8ba49bb06673"\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r 834c10340bce -r 11cb57237849 amrplusplus_wf.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrplusplus_wf.ga Thu Mar 24 04:16:47 2016 -0400 |
| [ |
| b'@@ -0,0 +1,547 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "amrplusplus_wf_pe", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": "AMR Database", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 200\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "c33b3302-86dd-4020-920b-e91904994b0b", \n+ "workflow_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": "Host Genome", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 285\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "828c1738-4db6-4548-89b8-85e68a00491a", \n+ "workflow_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 2, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": "FastQ Forward", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 370\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "1956acf3-af87-497d-bced-1dc18003b4ee", \n+ "workflow_outputs": []\n+ }, \n+ "3": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 3, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "label": "FastQ Reverse", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 200, \n+ "top": 455\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "0e020fbd-697d-4ebc-bd3d-0b45d5104b44", \n+ "workflow_outputs": []\n+ }, \n+ "4": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3", \n+ "id": 4, \n+ "input_connections": {\n+ "paired_end|paired_input_type_conditional|fastq_r1_in": {\n+ "id": 2, \n+ "output_name": "output"\n+ }, \n+ "paired_end|paired_input_type_conditional|fastq_r2_in": {\n+ "id": 3, \n+ "output_na'..b'{\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n+ "id": 10, \n+ "input_connections": {\n+ "input1": {\n+ "id": 0, \n+ "output_name": "output"\n+ }, \n+ "input2": {\n+ "id": 9, \n+ "output_name": "output1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Coverage Sampler", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 2184, \n+ "top": 200\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutput1": {\n+ "action_arguments": {\n+ "newname": "Coverage Results"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0", \n+ "tool_state": "{\\"input2\\": \\"null\\", \\"__page__\\": 0, \\"input1\\": \\"null\\", \\"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": "8305b84c-ceb2-41bb-9f07-4c7bedff5d0a", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output1", \n+ "uuid": "1db38476-e927-44aa-bac5-0ff46b81a2b7"\n+ }\n+ ]\n+ }, \n+ "11": {\n+ "annotation": "", \n+ "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", \n+ "id": 11, \n+ "input_connections": {\n+ "input1": {\n+ "id": 0, \n+ "output_name": "output"\n+ }, \n+ "sam_type|sampe_input2": {\n+ "id": 9, \n+ "output_name": "output1"\n+ }\n+ }, \n+ "inputs": [], \n+ "label": null, \n+ "name": "Snip Finder", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 2184, \n+ "top": 341\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutput1": {\n+ "action_arguments": {\n+ "newname": "Snip Results"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snp_caller/0.1.0", \n+ "tool_state": "{\\"sam_type\\": \\"{\\\\\\"best\\\\\\": \\\\\\"False\\\\\\", \\\\\\"mode\\\\\\": \\\\\\"paired_end\\\\\\", \\\\\\"__current_case__\\\\\\": 1, \\\\\\"sampe_input2\\\\\\": null}\\", \\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\"}", \n+ "tool_version": "0.1.0", \n+ "type": "tool", \n+ "uuid": "b7bac673-aed8-4abd-a873-f842b9497ac8", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output1", \n+ "uuid": "fb7fbbba-05bd-4477-a0ee-8e51bcbeddd2"\n+ }\n+ ]\n+ }\n+ }, \n+ "uuid": "6c6ee2ed-be38-4787-9a8e-5ab9a872a00e"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 834c10340bce -r 11cb57237849 repository_dependencies.xml --- a/repository_dependencies.xml Wed Mar 23 21:49:48 2016 -0400 +++ b/repository_dependencies.xml Thu Mar 24 04:16:47 2016 -0400 |
| b |
| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="A meta-package of tools needed to run the amrPlusPlus workflow"> - <repository changeset_revision="84f9d3911454" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b506e3641805" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |