Mercurial > repos > clairetn > detrprok_wf
changeset 1:20e004d0292b draft default tip
Uploaded
| author | clairetn |
|---|---|
| date | Mon, 20 May 2013 13:44:44 -0400 |
| parents | c265b11e7277 |
| children | |
| files | Galaxy-Workflow-Detrprok_wf.ga |
| diffstat | 1 files changed, 1190 insertions(+), 822 deletions(-) [+] |
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--- 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 @@ -2,27 +2,27 @@ "a_galaxy_workflow": "true", "annotation": "", "format-version": "0.1", - "name": "Detrprok_current", + "name": "Detrprok_wf", "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.", + "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.", "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" + "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.", + "name": "genome annotations" } ], "name": "Input dataset", "outputs": [], "position": { - "left": 166, - "top": 364 + "left": 200, + "top": 231.00001525878906 }, "tool_errors": null, "tool_id": null, - "tool_state": "{\"name\": \"positions list of all genome known annotations\"}", + "tool_state": "{\"name\": \"genome annotations\"}", "tool_version": null, "type": "data_input", "user_outputs": [] @@ -40,8 +40,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 215, - "top": 484 + "left": 205, + "top": 403.00001525878906 }, "tool_errors": null, "tool_id": null, @@ -51,30 +51,43 @@ "user_outputs": [] }, "2": { - "annotation": "", + "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", "id": 2, "input_connections": { - "inputFile": { + "formatType|inputFileName": { "id": 0, "output_name": "output" } }, - "inputs": [], - "name": "clean Gff", + "inputs": [ + { + "description": "runtime parameter for tool clean transcript file", + "name": "optionType" + } + ], + "name": "clean transcript file", "outputs": [ { "name": "outputFile", - "type": "gff3" + "type": "gtf" } ], "position": { - "left": 361, - "top": 327 + "left": 457, + "top": 218.00001525878906 }, - "post_job_actions": {}, + "post_job_actions": { + "RenameDatasetActionoutputFile": { + "action_arguments": { + "newname": "annotation selection" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFile" + } + }, "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_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CleanTranscriptFile/1.0.0", + "tool_state": "{\"optionType\": \"{\\\"type\\\": \\\"Yes\\\", \\\"value\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 0, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] @@ -97,13 +110,13 @@ } ], "position": { - "left": 418, - "top": 479 + "left": 428, + "top": 400.00001525878906 }, "post_job_actions": { "RenameDatasetActionoutput1": { "action_arguments": { - "newname": "Read alignments in SAM format" + "newname": "Read alignments (SAM format)" }, "action_type": "RenameDatasetAction", "output_name": "output1" @@ -111,13 +124,13 @@ }, "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_state": "{\"header\": \"\\\"True\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", "tool_version": "1.0.3", "type": "tool", "user_outputs": [] }, "4": { - "annotation": "Clusters annotated proximal genes into operons. \nParameter to be set: op_gap. \nGenes separated by a gap smaller than op_gap are clustered \n(suggested value: 10 to 150).", + "annotation": "Clusters annotated proximal genes into operons. Parameter to be set: op_gap. Genes separated by a gap smaller than op_gap are clustered (suggested value: 10 to 150).", "id": 4, "input_connections": { "formatType|inputFileName": { @@ -127,29 +140,25 @@ }, "inputs": [ { - "description": "runtime parameter for tool Clusterize", + "description": "runtime parameter for tool clusterize", "name": "distance" } ], - "name": "Clusterize", + "name": "clusterize", "outputs": [ { "name": "outputFileGff", "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" } ], "position": { - "left": 547, - "top": 297 + "left": 700, + "top": 200.00001525878906 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "Annotation with \"operon\"" + "newname": "Annotation with operon-like features" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" @@ -157,13 +166,13 @@ }, "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_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "5": { - "annotation": "Clusters overlapping or proximal reads to produce read clusters. \nParameter to be set: clust_gap. \nReads separated by a gap smaller than \nclust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart).", + "annotation": "Clusters overlapping or proximal reads to produce read clusters. Parameter to be set: clust_gap. Reads separated by a gap smaller than clust_gap are clustered (suggested value: 0 to 20 ; a value of 0 will cluster only overlapping reads while a value of 20 will cluster reads even if they are 20-nt apart)", "id": 5, "input_connections": { "formatType|inputFileName": { @@ -173,29 +182,25 @@ }, "inputs": [ { - "description": "runtime parameter for tool Clusterize", + "description": "runtime parameter for tool clusterize", "name": "distance" } ], - "name": "Clusterize", + "name": "clusterize", "outputs": [ { "name": "outputFileGff", "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" } ], "position": { - "left": 496, - "top": 596 + "left": 662, + "top": 505.00001525878906 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "Read clusters" + "newname": "Read clusters (with exon)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" @@ -203,31 +208,96 @@ }, "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_state": "{\"normalize\": \"\\\"False\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"sam\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/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. \nParameter to be set: RNA_gap.\nA read cluster separated from an annotation by a gap smaller than RNA_gap is selected (suggested value: 25).", + "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", "id": 6, "input_connections": { - "formatType2|inputFileName2": { + "inputFile": { "id": 4, "output_name": "outputFileGff" - }, - "formatType|inputFileName1": { + } + }, + "inputs": [], + "name": "remove exon lines", + "outputs": [ + { + "name": "outputFile", + "type": "gff3" + } + ], + "position": { + "left": 892, + "top": 221.00001525878906 + }, + "post_job_actions": { + "RenameDatasetActionoutputFile": { + "action_arguments": { + "newname": "Annotation with operon-like (without exon)" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", + "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "7": { + "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", + "id": 7, + "input_connections": { + "inputFile": { "id": 5, "output_name": "outputFileGff" } }, - "inputs": [ + "inputs": [], + "name": "remove exon lines", + "outputs": [ { - "description": "runtime parameter for tool Compare Overlapping Small Query", - "name": "OptionDistance" + "name": "outputFile", + "type": "gff3" } ], - "name": "Compare Overlapping Small Query", + "position": { + "left": 892, + "top": 505.00001525878906 + }, + "post_job_actions": { + "RenameDatasetActionoutputFile": { + "action_arguments": { + "newname": "Read clusters" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", + "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "8": { + "annotation": "Technical step: orders the features by increasing positions.", + "id": 8, + "input_connections": { + "formatType|inputFileName": { + "id": 6, + "output_name": "outputFile" + } + }, + "inputs": [], + "name": "collapse reads", "outputs": [ { "name": "outputFileGff", @@ -235,8 +305,100 @@ } ], "position": { - "left": 659, - "top": 417 + "left": 1072, + "top": 261.00001525878906 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Annotation list with operon-like feature" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "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\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "9": { + "annotation": "Selects read clusters that form new independent annotations. Parameter to be set: RNA_gap. Read clusters at a distance from existing annotations larger than RNA_gap are selected (suggested value: 25).", + "id": 9, + "input_connections": { + "formatType2|inputFileName2": { + "id": 8, + "output_name": "outputFileGff" + }, + "formatType|inputFileName1": { + "id": 7, + "output_name": "outputFile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool compare overlapping small query", + "name": "OptionDistance" + } + ], + "name": "compare overlapping small query", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 1197, + "top": 521.0000152587891 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Read clusters not overlapping annotation" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "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\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "10": { + "annotation": "Selects read clusters that overlap annotations in the same direction. Parameter to be set: RNA_gap. A read cluster separated from an annotation by a gap smaller than RNA_gap is selected. Caution: use same RNA_gap value as in previous step!", + "id": 10, + "input_connections": { + "formatType2|inputFileName2": { + "id": 8, + "output_name": "outputFileGff" + }, + "formatType|inputFileName1": { + "id": 7, + "output_name": "outputFile" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool compare overlapping small query", + "name": "OptionDistance" + } + ], + "name": "compare overlapping small query", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 1407, + "top": 328.00001525878906 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { @@ -249,31 +411,26 @@ }, "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_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\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, - "7": { - "annotation": "Selects read clusters that form new independent annotations. \nParameter to be set: RNA_gap.\nRead clusters at a distance from existing annotations larger than RNA_gap are selected. Caution: use same RNA_gap value as in previous step!", - "id": 7, + "11": { + "annotation": "Selection of read clusters that are antisense of an extended annotation. This step produces a first list of antisense candidates.", + "id": 11, "input_connections": { "formatType2|inputFileName2": { - "id": 4, + "id": 8, "output_name": "outputFileGff" }, "formatType|inputFileName1": { - "id": 5, + "id": 9, "output_name": "outputFileGff" } }, - "inputs": [ - { - "description": "runtime parameter for tool Compare Overlapping Small Query", - "name": "OptionDistance" - } - ], - "name": "Compare Overlapping Small Query", + "inputs": [], + "name": "compare overlapping small query", "outputs": [ { "name": "outputFileGff", @@ -281,13 +438,13 @@ } ], "position": { - "left": 742, - "top": 588 + "left": 1660, + "top": 531.0000152587891 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "Read clusters not overlapping annotation" + "newname": "first list of asRNA" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" @@ -295,21 +452,62 @@ }, "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_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, - "8": { + "12": { + "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation. This step produces a first list of small RNAs.", + "id": 12, + "input_connections": { + "formatType2|inputFileName2": { + "id": 8, + "output_name": "outputFileGff" + }, + "formatType|inputFileName1": { + "id": 9, + "output_name": "outputFileGff" + } + }, + "inputs": [], + "name": "compare overlapping small query", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 1665, + "top": 673 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "first list of sRNA" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "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\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"100\\\"}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "13": { "annotation": "Technical step: merging of annotations and their overlapping read clusters. This will be used to extend annotation.", - "id": 8, + "id": 13, "input_connections": { "input1": { - "id": 4, + "id": 8, "output_name": "outputFileGff" }, "queries_0|input2": { - "id": 6, + "id": 10, "output_name": "outputFileGff" } }, @@ -322,8 +520,8 @@ } ], "position": { - "left": 819, - "top": 294 + "left": 1725, + "top": 228.00001525878906 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -336,105 +534,27 @@ }, "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_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, - "9": { - "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. \nParameter to be set: RNA_gap.\nRead cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!", - "id": 9, + "14": { + "annotation": "Filters antisense RNAs based on their size. Parameter to be set: as_min_size. as_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", + "id": 14, "input_connections": { "formatType|inputFileName": { - "id": 8, - "output_name": "out_file1" + "id": 11, + "output_name": "outputFileGff" } }, "inputs": [ { - "description": "runtime parameter for tool Clusterize", - "name": "distance" - } - ], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" + "description": "runtime parameter for tool restrict from size", + "name": "OptionMin" } ], - "position": { - "left": 1036, - "top": 307 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "Extended annotation" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "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, - "top": 319 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "Extended annotation without \"exon\" lines" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "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": "Technical step: orders extended annotations by positions.", - "id": 11, - "input_connections": { - "formatType|inputFileName": { - "id": 10, - "output_name": "out_file1" - } - }, - "inputs": [], - "name": "collapse reads", + "name": "restrict from size", "outputs": [ { "name": "outputFileGff", @@ -442,81 +562,41 @@ } ], "position": { - "left": 973, - "top": 460 + "left": 1959.2166748046875, + "top": 548.4833526611328 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "Ordrered and extended annotation" + "newname": "asRNA list modified (filtered on their size)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" } }, "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_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", + "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, - "12": { - "annotation": "Splits extended annotations into UTRs, CDS and/or operon spacers.", - "id": 12, + "15": { + "annotation": "Filters small RNAs based on their size. Parameter to be set: sRNA_min_size. sRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).", + "id": 15, "input_connections": { - "referenciesFile": { - "id": 4, - "output_name": "outputFileGff" - }, - "transcriptsFile": { - "id": 11, + "formatType|inputFileName": { + "id": 12, "output_name": "outputFileGff" } }, - "inputs": [], - "name": "splitTranscriptGff", - "outputs": [ + "inputs": [ { - "name": "outputFile", - "type": "gff3" + "description": "runtime parameter for tool restrict from size", + "name": "OptionMin" } ], - "position": { - "left": 1221, - "top": 456 - }, - "post_job_actions": { - "RenameDatasetActionoutputFile": { - "action_arguments": { - "newname": "UTRs, CDSs and/or operons" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFile" - } - }, - "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 antisense of an extended annotation. \nThis step produces a first list of antisense candidates.", - "id": 13, - "input_connections": { - "formatType2|inputFileName2": { - "id": 11, - "output_name": "outputFileGff" - }, - "formatType|inputFileName1": { - "id": 7, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Compare Overlapping Small Query", + "name": "restrict from size", "outputs": [ { "name": "outputFileGff", @@ -524,40 +604,41 @@ } ], "position": { - "left": 1155, - "top": 617 + "left": 1954, + "top": 683 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "first list of asRNA" + "newname": "sRNA list modified (filtered on their size)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", - "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", + "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", + "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 4, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, - "14": { - "annotation": "Selection of read clusters that are outside and not in antisense of an extended annotation.\nThis step produces a first list of small RNAs.", - "id": 14, + "16": { + "annotation": "Extend annotations with overlapping or proximal read clusters in the same direction. Parameter to be set: RNA_gap. Read cluster and annotations separated by a gap smaller than RNA_gap are clustered. Caution: use the same RNA_gap value as previous step!", + "id": 16, "input_connections": { - "formatType2|inputFileName2": { - "id": 11, - "output_name": "outputFileGff" - }, - "formatType|inputFileName1": { - "id": 7, - "output_name": "outputFileGff" + "formatType|inputFileName": { + "id": 13, + "output_name": "out_file1" } }, - "inputs": [], - "name": "Compare Overlapping Small Query", + "inputs": [ + { + "description": "runtime parameter for tool clusterize", + "name": "distance" + } + ], + "name": "clusterize", "outputs": [ { "name": "outputFileGff", @@ -565,110 +646,27 @@ } ], "position": { - "left": 1068, - "top": 766 + "left": 1963, + "top": 257.00001525878906 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "first list of sRNA" + "newname": "Extended annotation (with exon)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallQuery/1.0.0", - "tool_state": "{\"OptionInclusionQuery\": \"\\\"True\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"True\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"gff3\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 3}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 1, \\\"OptionCA\\\": \\\"AntiSens\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "15": { - "annotation": "Counts reads overlapping UTRs, CDSs and/or operon spacers in order to compute read coverage (with a minimal overlapping region of 10 nt between read and genetic element). Output file of this step can be used to obtain read coverage of 5'UTRs, 3'UTRs, CDSs, or operon spacers.", - "id": 15, - "input_connections": { - "formatType2|inputFileName2": { - "id": 3, - "output_name": "output1" - }, - "formatType|inputFileName1": { - "id": 12, - "output_name": "outputFile" - } - }, - "inputs": [], - "name": "Compare Overlapping Small Reference", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 1417, - "top": 506 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "UTRs, CDSs and operons (with the number of overlapping reads)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/CompareOverlappingSmallRef/1.0.0", - "tool_state": "{\"OptionInclusionQuery\": \"\\\"False\\\"\", \"NotOverlapping\": \"\\\"False\\\"\", \"formatType\": \"{\\\"FormatInputFileName1\\\": \\\"gff3\\\", \\\"inputFileName1\\\": null, \\\"__current_case__\\\": 3}\", \"InvertMatch\": \"\\\"False\\\"\", \"__page__\": 0, \"OptionInclusionRef\": \"\\\"False\\\"\", \"OptionDistance\": \"{\\\"Dist\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"formatType2\": \"{\\\"FormatInputFileName2\\\": \\\"sam\\\", \\\"inputFileName2\\\": null, \\\"__current_case__\\\": 4}\", \"OptionPcOverlapQuery\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionMinOverlap\": \"{\\\"present\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"minOverlap\\\": \\\"10\\\"}\", \"OptionCollinearOrAntiSens\": \"{\\\"__current_case__\\\": 0, \\\"OptionCA\\\": \\\"Collinear\\\"}\", \"OptionPcOverlapRef\": \"{\\\"present\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "16": { - "annotation": "Filters antisense RNA candidates based on their number of overlapping reads.\nParameter to be set: as_min_reads.\nAntisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).", - "id": 16, - "input_connections": { - "formatType|inputFileName": { - "id": 13, - "output_name": "outputFileGff" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool select by tag", - "name": "OptionMin" - } - ], - "name": "select by tag", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 1461, - "top": 663 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "asRNA list modified (filtered on their number of overlapping reads)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", - "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 1, \\\"FormatInputFileName\\\": \\\"gff\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", + "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\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "17": { - "annotation": "Filters sRNA candidates based on their number of overlapping reads.\nParameter to be set: sRNA_min_reads.\nSmall RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).", + "annotation": "Filters antisense RNA candidates based on their number of overlapping reads. Parameter to be set: as_min_reads. Antisense RNAs with a number of reads higher than as_min_reads are selected (suggested value: 22).", "id": 17, "input_connections": { "formatType|inputFileName": { @@ -690,13 +688,13 @@ } ], "position": { - "left": 1389, - "top": 794 + "left": 2162.2166748046875, + "top": 554.4833526611328 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "sRNA list modified (filtered on their number of overlapping reads)" + "newname": "asRNA list modified (filtered on their number of overlapping reads)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" @@ -704,13 +702,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", - "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 2, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] }, "18": { - "annotation": "Technical step: coverage computation needs \"nbElements\" tag in place of \"nbOverlaps\".", + "annotation": "Filters sRNA candidates based on their number of overlapping reads. Parameter to be set: sRNA_min_reads. Small RNAs with a number of reads higher than sRNA_min_reads are selected (suggested value: 12).", "id": 18, "input_connections": { "formatType|inputFileName": { @@ -718,367 +716,6 @@ "output_name": "outputFileGff" } }, - "inputs": [], - "name": "change tag name", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 1696, - "top": 541 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "long 5'UTR list modified (tag \"nbElements\")" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/changeTagName/1.0.0", - "tool_state": "{\"__page__\": 0, \"Tag\": \"\\\"nbOverlaps\\\"\", \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"name\": \"\\\"nbElements\\\"\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "19": { - "annotation": "Clusters proximal antisense RNAs in the same direction.\nParameter to be set: RNA_merge.\nAntisense RNAs located less than RNA_merge apart are merged (suggestion: 50).", - "id": 19, - "input_connections": { - "formatType|inputFileName": { - "id": 16, - "output_name": "outputFileGff" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Clusterize", - "name": "distance" - } - ], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" - } - ], - "position": { - "left": 1658, - "top": 660 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "asRNA list modified (asRNA clusters)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "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": [] - }, - "20": { - "annotation": "Clusters proximal small RNAs in the same direction.\nParameter to be set: RNA_merge.\nSmall RNAs located less than RNA_merge apart are merged (suggestion: 50).", - "id": 20, - "input_connections": { - "formatType|inputFileName": { - "id": 17, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Clusterize", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - }, - { - "name": "outputFileLog", - "type": "txt" - } - ], - "position": { - "left": 1602, - "top": 797 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "sRNA list modified (sRNA clusters)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", - "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"distance\": \"\\\"50\\\"\", \"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": [] - }, - "21": { - "annotation": "Technical step: extracts 5'UTR features for following steps.", - "id": 21, - "input_connections": { - "input1": { - "id": 18, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Extract features", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1917, - "top": 547 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "first list of long 5'UTR" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Extract_features1", - "tool_state": "{\"column_choice\": \"{\\\"col\\\": \\\"2\\\", \\\"__current_case__\\\": 2, \\\"feature\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"utr5\\\"]}}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "22": { - "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", - "id": 22, - "input_connections": { - "input": { - "id": 19, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Select", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1859, - "top": 682 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "asRNA list modified (without \"exon\" lines)" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_errors": null, - "tool_id": "Grep1", - "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"pattern\": \"\\\"exon\\\"\"}", - "tool_version": "1.0.1", - "type": "tool", - "user_outputs": [] - }, - "23": { - "annotation": "Technical step: suppresses unwanted \"exon\" features created by the use of the distance option in the previous clustering step.", - "id": 23, - "input_connections": { - "input": { - "id": 20, - "output_name": "outputFileGff" - } - }, - "inputs": [], - "name": "Select", - "outputs": [ - { - "name": "out_file1", - "type": "input" - } - ], - "position": { - "left": 1804, - "top": 813 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "sRNA list modified (without \"exon\" lines)" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "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": [] - }, - "24": { - "annotation": "Filters 5'UTR based on their size.\nParameter to be set: 5UTR_min_size.\n5'UTRs larger than 5UTR_min_size are selected (suggestion value: 50).", - "id": 24, - "input_connections": { - "formatType|inputFileName": { - "id": 21, - "output_name": "out_file1" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool restrict from size", - "name": "OptionMin" - } - ], - "name": "restrict from size", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 2132, - "top": 570 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "long 5'UTR list modified (filtered on their size)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", - "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "25": { - "annotation": "Filters antisense RNAs based on their size.\nParameter to be set: as_min_size.\nas_min_size is the minimal size for calling an antisense RNA (suggestion: 50).", - "id": 25, - "input_connections": { - "formatType|inputFileName": { - "id": 22, - "output_name": "out_file1" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool restrict from size", - "name": "OptionMin" - } - ], - "name": "restrict from size", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 2085, - "top": 691 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "asRNA list modified (filtered on their size)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", - "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "26": { - "annotation": "Filters small RNAs based on their size.\nParameter to be set: sRNA_min_size.\nsRNA_min_size is the minimal size for calling a small RNA (suggestion: 50).", - "id": 26, - "input_connections": { - "formatType|inputFileName": { - "id": 23, - "output_name": "out_file1" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool restrict from size", - "name": "OptionMin" - } - ], - "name": "restrict from size", - "outputs": [ - { - "name": "outputFileGff", - "type": "gff3" - } - ], - "position": { - "left": 2017, - "top": 824 - }, - "post_job_actions": { - "RenameDatasetActionoutputFileGff": { - "action_arguments": { - "newname": "sRNA list modified (filtered on their size)" - }, - "action_type": "RenameDatasetAction", - "output_name": "outputFileGff" - } - }, - "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/restrictFromSize/1.0.0", - "tool_state": "{\"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\"}", - "tool_version": "1.0.0", - "type": "tool", - "user_outputs": [] - }, - "27": { - "annotation": "Filters long 5' UTR candidates based on their number of overlapping reads.\nParameter to be set: 5UTR_min_reads.\nLong 5'UTR with a number of reads higher than 5UTR_min_reads is selected (suggested value: 10).", - "id": 27, - "input_connections": { - "formatType|inputFileName": { - "id": 24, - "output_name": "outputFileGff" - } - }, "inputs": [ { "description": "runtime parameter for tool select by tag", @@ -1093,13 +730,13 @@ } ], "position": { - "left": 2344, - "top": 577 + "left": 2168, + "top": 687 }, "post_job_actions": { "RenameDatasetActionoutputFileGff": { "action_arguments": { - "newname": "long 5'UTR list modified (filtered on their number of overlapping reads)" + "newname": "sRNA list modified (filtered on their number of overlapping reads)" }, "action_type": "RenameDatasetAction", "output_name": "outputFileGff" @@ -1107,20 +744,519 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/SelectByTag/1.0.0", - "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/share/apps/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", + "tool_state": "{\"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 2, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"OptionMin\": \"{\\\"minimum\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"min\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"Tag\": \"\\\"nbElements\\\"\", \"OptionMax\": \"{\\\"maximum\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"OptionValue\": \"{\\\"Value\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"OptionDefault\": \"{\\\"default\\\": \\\"Yes\\\", \\\"defaultValue\\\": \\\"0.0\\\", \\\"__current_case__\\\": 0}\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "19": { + "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", + "id": 19, + "input_connections": { + "inputFile": { + "id": 16, + "output_name": "outputFileGff" + } + }, + "inputs": [], + "name": "remove exon lines", + "outputs": [ + { + "name": "outputFile", + "type": "gff3" + } + ], + "position": { + "left": 2176, + "top": 274.00001525878906 + }, + "post_job_actions": { + "RenameDatasetActionoutputFile": { + "action_arguments": { + "newname": "Extended annotation" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFile" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/removeExonLines/1.0.0", + "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "20": { + "annotation": "Clusters proximal antisense RNAs in the same direction. Parameter to be set: RNA_merge. Antisense RNAs located less than RNA_merge apart are merged (suggestion: 50).", + "id": 20, + "input_connections": { + "formatType|inputFileName": { + "id": 17, + "output_name": "outputFileGff" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool clusterize", + "name": "distance" + } + ], + "name": "clusterize", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 2395.38330078125, + "top": 567.8166809082031 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "asRNA list modified (asRNA clusters)" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "tool_errors": null, + "tool_id": "toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/MergingDataClusterize/1.0.0", + "tool_state": "{\"normalize\": \"\\\"False\\\"\", \"colinear\": \"\\\"True\\\"\", \"__page__\": 0, \"formatType\": \"{\\\"inputFileName\\\": null, \\\"__current_case__\\\": 3, \\\"FormatInputFileName\\\": \\\"gff3\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "21": { + "annotation": "Clusters proximal small RNAs in the same direction. Parameter to be set: RNA_merge. Small RNAs located less than RNA_merge apart are merged (suggestion: 50).", + "id": 21, + "input_connections": { + "formatType|inputFileName": { + "id": 18, + "output_name": "outputFileGff" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool clusterize", + "name": "distance" + } + ], + "name": "clusterize", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 2371, + "top": 686 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "sRNA list modified (sRNA clusters)" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "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\\\"}\", \"distance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"colinear\": \"\\\"True\\\"\", \"chromInfo\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "22": { + "annotation": "Technical step: orders extended annotations by positions.", + "id": 22, + "input_connections": { + "formatType|inputFileName": { + "id": 19, + "output_name": "outputFile" + } + }, + "inputs": [], + "name": "collapse reads", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 2387, + "top": 287.00001525878906 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Ordrered and extended annotation" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFileGff" + } + }, + "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\": \"\\\"/srv/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"strand\": \"\\\"False\\\"\"}", + "tool_version": "1.0.0", + "type": "tool", + "user_outputs": [] + }, + "23": { + "annotation": "Technical step: suppresses unwanted \"exon\" features created by the previous clustering step.", + "id": 23, + "input_connections": { + "inputFile": { + "id": 20, + "output_name": "outputFileGff" + } + }, + "inputs": [], + "name": "remove exon lines", + "outputs": [ + { + "name": "outputFile", + "type": "gff3" + } + ], + "position": { + "left": 2591.88330078125, + "top": 564.8166809082031 + }, + "post_job_actions": { + "RenameDatasetActionoutputFile": { + "action_arguments": { + "newname": "asRNA list modified (without \"exon\" lines)" + }, + "action_type": "RenameDatasetAction", + "output_name": "outputFile" + } + }, + "tool_errors": null, + 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