| Next changeset 1:20e004d0292b (2013-05-20) |
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Commit message:
Uploaded |
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added:
Galaxy-Workflow-Detrprok_wf.ga |
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| diff -r 000000000000 -r c265b11e7277 Galaxy-Workflow-Detrprok_wf.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Detrprok_wf.ga Mon Mar 25 05:51:08 2013 -0400 |
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| b'@@ -0,0 +1,1301 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "Detrprok_current", \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+ "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+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 166, \n+ "top": 364\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"positions list of all genome known annotations\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "Select here the bam file resulting from the mapping of RNA-seq reads on the genome sequence. You may use Bowtie or another mapper (use appropriate mapping option to retain only uniquely mapping reads).", \n+ "name": "read alignments on genome"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 215, \n+ "top": 484\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"read alignments on genome\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "2": {\n+ "annotation": "", \n+ "id": 2, \n+ "input_connections": {\n+ "inputFile": {\n+ "id": 0, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "clean Gff", \n+ "outputs": [\n+ {\n+ "name": "outputFile", \n+ "type": "gff3"\n+ }\n+ ], \n+ "position": {\n+ "left": 361, \n+ "top": 327\n+ }, \n+ "post_job_actions": {}, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0", \n+ "tool_state": "{\\"__page__\\": 0, \\"type\\": \\"\\\\\\"tRNA,rRNA,ncRNA,CDS\\\\\\"\\", \\"inputFile\\": \\"null\\"}", \n+ "tool_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "3": {\n+ "annotation": "Technical step (format change).", \n+ "id": 3, \n+ "input_connections": {\n+ "input1": {\n+ "id": 1, \n+ "output_name": "output"\n+ }\n+ }, \n+ "inputs": [], \n+ "name": "BAM-to-SAM", \n+ "outputs": [\n+ {\n+ "name": "output1", \n+ "type": "sam"\n+ }\n+ '..b'ts": [], \n+ "name": "colorGff", \n+ "outputs": [\n+ {\n+ "name": "outputFile", \n+ "type": "gff"\n+ }\n+ ], \n+ "position": {\n+ "left": 2525, \n+ "top": 610\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutputFile": {\n+ "action_arguments": {\n+ "newname": "final long 5\'UTR list (with the annotation color)"\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_version": "1.0.0", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |