comparison smart_toolShed/SMART/galaxy/ConvertTranscriptFile_SamToGff3.xml @ 0:e0f8dcca02ed

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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-1:000000000000 0:e0f8dcca02ed
1 <tool id="ConvertTranscriptFile_SamToGff3" name="Sam -> Gff3">
2 <description>Convert Sam File to Gff3 File.</description>
3 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFile -f sam -o $outputFile -g gff3 yes 2>$logFile </command>
4 <inputs>
5 <param name="inputFile" type="data" label="Input File" format="sam"/>
6 </inputs>
7
8 <outputs>
9 <data format="gff3" name="outputFile" label="[sam -> gff3] Output File"/>
10 <data format="txt" name="logFile" label="[sam -> gff3] Log File"/>
11 </outputs>
12
13 <help>
14 </help>
15 </tool>