Mercurial > repos > yufei-luo > s_mart

diff smart_toolShed/SMART/galaxy/ConvertTranscriptFile_SamToGff2.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/ConvertTranscriptFile_SamToGff2.xml	Thu Jan 17 10:52:14 2013 -0500
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+<tool id="ConvertTranscriptFile_SamToGff2" name="Sam -> Gff2">
+  <description>Convert Sam File to Gff2 File.</description>
+  <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff2 yes 2>$logFile </command>
+  <inputs>
+    <param name="inputFile" type="data" label="Input File" format="sam"/>
+  </inputs>
+
+  <outputs>
+    <data format="gff" name="outputFile" label="[sam -> gff2] Output File"/>
+    <data format="txt" name="logFile" label="[sam -> gff2] Log File"/>
+  </outputs>
+
+  <help>
+  </help>
+</tool>