| Previous changeset 0:c265b11e7277 (2013-03-25) |
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Commit message:
Uploaded |
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modified:
Galaxy-Workflow-Detrprok_wf.ga |
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| diff -r c265b11e7277 -r 20e004d0292b Galaxy-Workflow-Detrprok_wf.ga --- a/Galaxy-Workflow-Detrprok_wf.ga Mon Mar 25 05:51:08 2013 -0400 +++ b/Galaxy-Workflow-Detrprok_wf.ga Mon May 20 13:44:44 2013 -0400 |
| [ |
| b'@@ -2,27 +2,27 @@\n "a_galaxy_workflow": "true", \n "annotation": "", \n "format-version": "0.1", \n- "name": "Detrprok_current", \n+ "name": "Detrprok_wf", \n "steps": {\n "0": {\n- "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", \n+ "annotation": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", \n "id": 0, \n "input_connections": {}, \n "inputs": [\n {\n- "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI. Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", \n- "name": "positions list of all genome known annotations"\n+ "description": "Select here annotation file containing coding genes, tRNAs, rRNAs and known ncRNAs. You can download it from GJI (http://genome.jgi.doe.gov) or NCBI (http://ftp.ncbi.nih.gov/genomes/Bacteria). Caution: 1srt column should have exactly the same identifier as the genome sequence used for mapping.", \n+ "name": "genome annotations"\n }\n ], \n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 166, \n- "top": 364\n+ "left": 200, \n+ "top": 231.00001525878906\n }, \n "tool_errors": null, \n "tool_id": null, \n- "tool_state": "{\\"name\\": \\"positions list of all genome known annotations\\"}", \n+ "tool_state": "{\\"name\\": \\"genome annotations\\"}", \n "tool_version": null, \n "type": "data_input", \n "user_outputs": []\n@@ -40,8 +40,8 @@\n "name": "Input dataset", \n "outputs": [], \n "position": {\n- "left": 215, \n- "top": 484\n+ "left": 205, \n+ "top": 403.00001525878906\n }, \n "tool_errors": null, \n "tool_id": null, \n@@ -51,30 +51,43 @@\n "user_outputs": []\n }, \n "2": {\n- "annotation": "", \n+ "annotation": "Select here the GFF file features that will be considered as initial annotations. Any term added here will cause pre-existing features with this term not to be predicted again by the workflow. Please use a comma separated list and use \\"CDS\\" rather than \\"gene\\" for protein coding genes. Suggested value: rRNA,tRNA,ncRNA,CDS", \n "id": 2, \n "input_connections": {\n- "inputFile": {\n+ "formatType|inputFileName": {\n "id": 0, \n "output_name": "output"\n }\n }, \n- "inputs": [], \n- "name": "clean Gff", \n+ "inputs": [\n+ {\n+ "description": "runtime parameter for tool clean transcript file", \n+ "name": "optionType"\n+ }\n+ ], \n+ "name": "clean transcript file", \n "outputs": [\n {\n "name": "outputFile", \n- "type": "gff3"\n+ "type": "gtf"\n }\n ], \n "position": {\n- "left": 361, \n- "top": 327\n+ "left": 457, \n+ "top": 218.000'..b' "post_job_actions": {\n- "RenameDatasetActionoutputFile": {\n- "action_arguments": {\n- "newname": "final long 5\'UTR list (with the annotation color)"\n+ "newname": "long 5_extensions list"\n }, \n "action_type": "RenameDatasetAction", \n "output_name": "outputFile"\n }\n }, \n "tool_errors": null, \n- "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"referenciesFile\\": \\"null\\", \\"RGBcolor\\": \\"\\\\\\"255 105 180\\\\\\"\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "31": {\n- "annotation": "Technical step: changes \\"transcript\\" for \\"asRNA\\" in the 3rd column.", \n- "id": 31, \n- "input_connections": {\n- "inputFile": {\n- "id": 28, \n- "output_name": "outputFile"\n- }\n- }, \n- "inputs": [], \n- "name": "change gff Features", \n- "outputs": [\n- {\n- "name": "outputFile", \n- "type": "gff"\n- }\n- ], \n- "position": {\n- "left": 2542, \n- "top": 727\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutputFile": {\n- "action_arguments": {\n- "newname": "final asRNA list (with the annotation color)"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "outputFile"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"inputFeature\\": \\"\\\\\\"transcript\\\\\\"\\", \\"outputFeature\\": \\"\\\\\\"asRNA\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n- "tool_version": "1.0.0", \n- "type": "tool", \n- "user_outputs": []\n- }, \n- "32": {\n- "annotation": "Technical step: changes \\"transcript\\" for \\"sRNA\\" in the 3rd column.", \n- "id": 32, \n- "input_connections": {\n- "inputFile": {\n- "id": 29, \n- "output_name": "outputFile"\n- }\n- }, \n- "inputs": [], \n- "name": "change gff Features", \n- "outputs": [\n- {\n- "name": "outputFile", \n- "type": "gff"\n- }\n- ], \n- "position": {\n- "left": 2464, \n- "top": 827\n- }, \n- "post_job_actions": {\n- "RenameDatasetActionoutputFile": {\n- "action_arguments": {\n- "newname": "final sRNA list (with the annotation color)"\n- }, \n- "action_type": "RenameDatasetAction", \n- "output_name": "outputFile"\n- }\n- }, \n- "tool_errors": null, \n- "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeGffFeatures/1.0.0", \n- "tool_state": "{\\"__page__\\": 0, \\"inputFeature\\": \\"\\\\\\"transcript\\\\\\"\\", \\"outputFeature\\": \\"\\\\\\"sRNA\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/colorGff/1.0.0", \n+ "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"referenciesFile\\": \\"null\\", \\"RGBcolor\\": \\"\\\\\\"255 105 180\\\\\\"\\"}", \n "tool_version": "1.0.0", \n "type": "tool", \n "user_outputs": []\n' |