# HG changeset patch # User clairetn # Date 1364158434 14400 # Node ID bb71a378053af9d6d1865f96ef376650c0ed4e3e # Parent f0ca0981eb86553d642241d4c432c998264fb5f3 Deleted selected files diff -r f0ca0981eb86 -r bb71a378053a Galaxy-Workflow-_DetR_Prok_v3__.ga --- a/Galaxy-Workflow-_DetR_Prok_v3__.ga Sun Mar 24 16:53:14 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1003 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "This workflow aims at identify 3 kinds of ncRNA in prokaryotic sequences. \n\nIt need as entries the alignment file of reads on a genomic sequence (bam format) and the annotation file of the genomic sequence (gff format).", - "format-version": "0.1", - "name": "\"DetR'Prok_v3''", - "steps": { - "0": { - "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.", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "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.", - "name": "positions list of all genome known annotations" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 160.9000244140625, - "top": 353.75 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"positions list of all genome known annotations\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "1": { - "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).", - "id": 1, - "input_connections": {}, - "inputs": [ - { - "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).", - "name": "read alignments on genome" - } - ], - "name": "Input dataset", - "outputs": [], - "position": { - "left": 215.9000244140625, - "top": 484.98333740234375 - }, - "tool_errors": null, - "tool_id": null, - "tool_state": "{\"name\": \"read alignments on genome\"}", - "tool_version": null, - "type": "data_input", - "user_outputs": [] - }, - "2": { - "annotation": "", - "id": 2, - "input_connections": { - "inputFile": { - "id": 0, - "output_name": "output" - } - }, - "inputs": [], - "name": "clean Gff", - "outputs": [ - { - "name": "outputFile", - "type": "gff3" - } - ], - "position": { - "left": 361.11669921875, - "top": 327.0833282470703 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/cleanGff/1.0.0", - "tool_state": "{\"__page__\": 0, \"type\": \"\\\"tRNA,rRNA,ncRNA,CDS\\\"\", \"inputFile\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "3": { - "annotation": "Technical step (format change).", - "id": 3, - "input_connections": { - "input1": { - "id": 1, - "output_name": "output" - } - }, - "inputs": [], - "name": "BAM-to-SAM", - "outputs": [ - { - "name": "output1", - "type": "sam" - } - ], - "position": { - "left": 418.666748046875, - "top": 479.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "bam_to_sam", - "tool_state": "{\"header\": \"\\\"False\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", - "tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - }, - "4": { - "annotation": "In box, enter the maximal intergenic distance used for operon definition. This distance depends on the gene density of the organism (try 30 for Escherichia coli, 150 for Vibrio splendidus).", - "id": 4, - "input_connections": { - "formatType|inputFileName": { - "id": 2, - "output_name": "outputFile" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Clusterize", - "name": "distance" - } - ], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" - } - ], - "position": { - "left": 547.0167236328125, - "top": 297.6999969482422 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", - "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "5": { - "annotation": "In box, enter the maximal distance used to cluster reads of same direction for read clusters definition. This distance depends on the deepness of the RNAseq (ex. a value of 0 will cluster only overlapping reads and a value of 20 will cluster reads even if they are 20-nt apart).", - "id": 5, - "input_connections": { - "formatType|inputFileName": { - "id": 3, - "output_name": "output1" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Clusterize", - "name": "distance" - } - ], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" - } - ], - "position": { - "left": 496.433349609375, - "top": 596.9833374023438 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", - "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 5, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "6": { - "annotation": "Selects read clusters that overlap annotations in the same direction. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart).", - "id": 6, - "input_connections": { - "formatType2|inputFileName2": { - "id": 4, - "output_name": "outputFileGff" - }, - "formatType|inputFileName1": { - "id": 5, - "output_name": "outputFileGff" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Compare Overlapping Small Query", - "name": "OptionDistance" - } - ], - "name": "Compare Overlapping Small Query", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 655.2000732421875, - "top": 433.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", - "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "7": { - "annotation": "Selects read clusters that form new independent annotations. In box, enter minimal distance between cluster and existing annotations. Caution: use same value as in previous step! (15 was suggested)", - "id": 7, - "input_connections": { - "formatType2|inputFileName2": { - "id": 4, - "output_name": "outputFileGff" - }, - "formatType|inputFileName1": { - "id": 5, - "output_name": "outputFileGff" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Compare Overlapping Small Query", - "name": "OptionDistance" - } - ], - "name": "Compare Overlapping Small Query", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 742.2000732421875, - "top": 588.75 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", - "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"Dist\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 1}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "8": { - "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be use to define transcription units.", - "id": 8, - "input_connections": { - "input1": { - "id": 4, - "output_name": "outputFileGff" - }, - "queries_0|input2": { - "id": 6, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Concatenate datasets", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 819.9666748046875, - "top": 294.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "cat1", - "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "9": { - "annotation": "Selects read clusters that overlap annotations in the same direction. In box, enter maximal distance to associate a cluster to an annotation (ex. a distance of 15 nt will associate a read cluster to an annotation even if they are 15-nt apart). This step defines extended CDS.", - "id": 9, - "input_connections": { - "formatType|inputFileName": { - "id": 8, - "output_name": "out_file1" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Clusterize", - "name": "distance" - } - ], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" - } - ], - "position": { - "left": 1036.7333679199219, - "top": 307.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", - "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"log\": \"\\\"False\\\"\", \"__page__\": 0, \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "10": { - "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", - "id": 10, - "input_connections": { - "input": { - "id": 9, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Select", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1232.5000610351562, - "top": 319.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "Grep1", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"exon\\\"\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "11": { - "annotation": "List of transcription units (ordered by positions).", - "id": 11, - "input_connections": { - "formatType|inputFileName": { - "id": 10, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "collapse reads", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 973.2667236328125, - "top": 460.98333740234375 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/collapseReads/1.0.0", - "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "12": { - "annotation": "Splits extended CDS into UTRs, CDS and/or operon spacers.", - "id": 12, - "input_connections": { - "referenciesFile": { - "id": 4, - "output_name": "outputFileGff" - }, - "transcriptsFile": { - "id": 11, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "splitTranscriptGff", - "outputs": [ - { - "name": "outputFile", - "type": "gff3" - } - ], - "position": { - "left": 1215.2833862304688, - "top": 452.01666259765625 - }, - "post_job_actions": {}, - "tool_errors": null, - "tool_id": "testtoolshed.g2.bx.psu.edu/repos/clairetn/detrprok_scripts/splitTranscriptGff/1.0.0", - "tool_state": "{\"transcriptsFile\": \"null\", \"__page__\": 0, \"referenciesFile\": \"null\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "13": { - "annotation": "Selection of read clusters that are outside and not in antisense of extended CDS. 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