Mercurial > repos > clairetn > detrprok_wf
changeset 0:c265b11e7277 draft
Uploaded
| author | clairetn |
|---|---|
| date | Mon, 25 Mar 2013 05:51:08 -0400 |
| parents | |
| children | 20e004d0292b |
| files | Galaxy-Workflow-Detrprok_wf.ga |
| diffstat | 1 files changed, 1301 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-Detrprok_wf.ga Mon Mar 25 05:51:08 2013 -0400 @@ -0,0 +1,1301 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "", + "format-version": "0.1", + "name": "Detrprok_current", + "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": 166, + "top": 364 + }, + "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, + "top": 484 + }, + "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, + "top": 327 + }, + "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, + "top": 479 + }, + "post_job_actions": { + "RenameDatasetActionoutput1": { + "action_arguments": { + "newname": "Read alignments in SAM format" + }, + "action_type": "RenameDatasetAction", + "output_name": "output1" + } + }, + "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": "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).", + "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, + "top": 297 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Annotation with \"operon\"" + }, + "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": [] + }, + "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).", + "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, + "top": 596 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Read 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\": \"{\\\"__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. \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).", + "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": 659, + "top": 417 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "Read clusters 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\": \"\\\"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. \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, + "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, + "top": 588 + }, + "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\\\": \\\"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 used to extend annotation.", + "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, + "top": 294 + }, + "post_job_actions": { + "RenameDatasetActionout_file1": { + "action_arguments": { + "newname": "Annotations and read clusters overlapping them" + }, + "action_type": "RenameDatasetAction", + "output_name": "out_file1" + } + }, + "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": "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, + "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, + "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", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 973, + "top": 460 + }, + "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\": \"\\\"/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 annotations 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": 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", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 1155, + "top": 617 + }, + "post_job_actions": { + "RenameDatasetActionoutputFileGff": { + "action_arguments": { + "newname": "first list of asRNA" + }, + "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_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, + "input_connections": { + "formatType2|inputFileName2": { + "id": 11, + "output_name": "outputFileGff" + }, + "formatType|inputFileName1": { + "id": 7, + "output_name": "outputFileGff" + } + }, + "inputs": [], + "name": "Compare Overlapping Small Query", + "outputs": [ + { + "name": "outputFileGff", + "type": "gff3" + } + ], + "position": { + "left": 1068, + "top": 766 + }, + "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\": \"\\\"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\": 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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, 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