Mercurial > repos > yufei-luo > s_mart

diff smart_toolShed/SMART/galaxy/cleanGff.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/galaxy/cleanGff.xml	Thu Jan 17 10:52:14 2013 -0500
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+<tool id="cleanGff" name="clean Gff">
+	  <description>Cleans a GFF file as given by NCBI and outpus a Gff3 file.</description>
+	  <command interpreter="python"> ../Java/Python/cleanGff.py -i $inputFile 
+		  -t $type 
+		  -o $outputFile
+	  </command>
+
+	      <inputs>
+		      <param name="inputFile" type="data" label="Input File" format="gff"/>
+		      <param name="type" type="text" value="tRNA,rRNA,ncRNA,CDS" label="tag option, compulsory option" help="lists of comma separated types that you want to keep.EX: ncRNA,tRNA,rRNA,CDS"/>
+	      </inputs>
+
+	      <outputs>
+	          <data format="gff3" name="outputFile" label="[cleanGff] Output File"/>
+	      </outputs>
+
+</tool>
+