| Previous changeset 3:402c3f0fe807 (2012-10-18) Next changeset 5:b321e0517be3 (2014-05-22) |
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Commit message:
Uploaded workflow from vcf file to CAPS |
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added:
Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga |
| b |
| diff -r 402c3f0fe807 -r be070a68521e Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga Thu Oct 18 19:47:07 2012 -0400 |
| [ |
| b'@@ -0,0 +1,273 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "CAPS Marker Design from VCF", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Multi fasta Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 214, \n+ "top": 225\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Multi fasta Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input VCF Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 174, \n+ "top": 592\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input VCF Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n+ "input_connections": {\n+ "inputVcf": {\n+ "id": 1, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Convert vcf to gff", \n+ "outputs": [\n+ {\n+ "name": "outputfile", \n+ "type": "gff3"\n+ }\n+ ], \n+ "position": {\n+ "left": 460.99998474121094, \n+ "top": 568\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/vcf2gff_1/1.0.0", \n+ "tool_state": "{\\"inputVcf\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__page__\\": 0}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "3": {\n+ "annotation": "Detect resitriction polymorphisms", \n+ "id": 3, \n+ "input_connections": {\n+ "inputFasta": {\n+ "id": 0, \n+ "output_name": "output"\n+ }, \n+ 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"newname": "PrimerPairs"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "primer_outputfile"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", \n+ "tool_state": "{\\"__page__\\": 0, \\"inputTargetfile\\": \\"null\\", \\"inputfastaFile\\": \\"null\\", \\"min_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\", \\"inputSNPfile\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"max_size\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"RuntimeValue\\\\\\"}\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "6": {\n+ "annotation": "", \n+ "id": 6, \n+ "input_connections": {\n+ "input": {\n+ "id": 5, \n+ "output_name": "primer_outputfile"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Select", \n+ "outputs": [\n+ {\n+ "name": "out_file1", \n+ "type": "input"\n+ }\n+ ], \n+ "position": {\n+ "left": 1406, \n+ "top": 382\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionout_file1": {\n+ "action_arguments": {\n+ "newname": "SuccessfulDesignSets"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "Grep1", \n+ "tool_state": "{\\"__page__\\": 0, \\"input\\": \\"null\\", \\"invert\\": \\"\\\\\\"true\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"pattern\\": \\"\\\\\\"NONE\\\\\\"\\"}", \n+ "tool_version": "1.0.1", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "7": {\n+ "annotation": "", \n+ "id": 7, \n+ "input_connections": {\n+ "inputFile": {\n+ "id": 6, \n+ "output_name": "out_file1"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "Unique", \n+ "outputs": [\n+ {\n+ "name": "outputfile", \n+ "type": "txt"\n+ }\n+ ], \n+ "position": {\n+ "left": 1625.9999389648438, \n+ "top": 382\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutputfile": {\n+ "action_arguments": {\n+ "newname": "UniquePrimerSets"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "outputfile"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", \n+ "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |