| Previous changeset 4:d1896971200b (2016-03-27) Next changeset 6:86dc721b6860 (2016-06-22) |
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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty |
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modified:
README.rst repository_dependencies.xml |
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added:
amrplusplus_workflow.ga workflow.jpeg |
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removed:
amrplusplus_pe.ga |
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| diff -r d1896971200b -r 04f9c20fecf8 README.rst --- a/README.rst Sun Mar 27 02:42:55 2016 -0400 +++ b/README.rst Wed Jun 22 00:27:14 2016 -0400 |
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| @@ -1,7 +1,9 @@ What is this? ============= -This is a suite that contains a collection of tools which can be used to analyze metagenomic sequence data. +A suite that contains a collection of tools and workflows which can be used to identify and characterize resistance and virulence genes. + +.. image:: https://raw.githubusercontent.com/cdeanj/galaxytools/master/workflows/amrplusplus/workflow.jpeg Availability ============ |
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| diff -r d1896971200b -r 04f9c20fecf8 amrplusplus_pe.ga --- a/amrplusplus_pe.ga Sun Mar 27 02:42:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,547 +0,0 @@\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- 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| diff -r d1896971200b -r 04f9c20fecf8 amrplusplus_workflow.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrplusplus_workflow.ga Wed Jun 22 00:27:14 2016 -0400 |
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| b'@@ -0,0 +1,595 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "aa", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "content_id": null, \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "FASTQ Forward"\n+ }\n+ ], \n+ "label": "FASTQ Forward", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 252, \n+ "top": 323\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": "9c1f5852-9697-40e2-bc6f-7ac65ad647ce", \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": "FASTQ Reverse"\n+ }\n+ ], \n+ "label": "FASTQ Reverse", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 251, \n+ "top": 399\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"FASTQ Reverse\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "uuid": "030bf3fc-ee71-46c4-bfcf-8d963c04a478", \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": "Host Genome"\n+ }\n+ ], \n+ "label": "Host Genome", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 498, \n+ "top": 200\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": "95f884fc-215e-4d54-8212-e43be8a779b5", \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": "AMR Database"\n+ }\n+ ], \n+ "label": "AMR Database", \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 1086, \n+ "top": 560\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": "8a65e391-b837-41ef-9575-bedf5294da9e", \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": 0, \n+ "output_name": "output"\n+ }, \n+ "paired_end|paired_input_type_conditional|fastq_r2_in": {\n+ "id": 1, \n+ "output_name": "output"\n+ '..b' "output_name": "output1"\n+ }\n+ }, \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool BAM-to-SAM", \n+ "name": "input1"\n+ }\n+ ], \n+ "label": null, \n+ "name": "BAM-to-SAM", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "sam"\n+ }\n+ ], \n+ "position": {\n+ "left": 1507.5, \n+ "top": 433\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0", \n+ "tool_shed_repository": {\n+ "changeset_revision": "af7c50162f0b", \n+ "name": "bam_to_sam", \n+ "owner": "devteam", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"header\\": \\"\\\\\\"-h\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"__page__\\": 0}", \n+ "tool_version": "2.0", \n+ "type": "tool", \n+ "uuid": "5076f37b-5da6-44a3-a3b2-f4172d547dc3", \n+ "workflow_outputs": [\n+ {\n+ "label": null, \n+ "output_name": "output1", \n+ "uuid": "4b52f2d0-1a66-408a-bc99-0da79cc8542f"\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+ "id": 3, \n+ "output_name": "output"\n+ }, \n+ "input2": {\n+ "id": 10, \n+ "output_name": "output1"\n+ }\n+ }, \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool Coverage Sampler", \n+ "name": "input2"\n+ }, \n+ {\n+ "description": "runtime parameter for tool Coverage Sampler", \n+ "name": "input1"\n+ }\n+ ], \n+ "label": null, \n+ "name": "Coverage Sampler", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "tabular"\n+ }\n+ ], \n+ "position": {\n+ "left": 1618.5, \n+ "top": 553\n+ }, \n+ "post_job_actions": {\n+ "HideDatasetActionoutput1": {\n+ "action_arguments": {}, \n+ "action_type": "HideDatasetAction", \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_shed_repository": {\n+ "changeset_revision": "72901052a829", \n+ "name": "coverage_sampler", \n+ "owner": "chrisd", \n+ "tool_shed": "toolshed.g2.bx.psu.edu"\n+ }, \n+ "tool_state": "{\\"input2\\": 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| diff -r d1896971200b -r 04f9c20fecf8 repository_dependencies.xml --- a/repository_dependencies.xml Sun Mar 27 02:42:55 2016 -0400 +++ b/repository_dependencies.xml Wed Jun 22 00:27:14 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="cf39a64bc9fe" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="29818e0c3fb5" name="amrplusplus_suite" owner="chrisd" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r d1896971200b -r 04f9c20fecf8 workflow.jpeg |
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| Binary file workflow.jpeg has changed |
