view smart_toolShed/SMART/galaxy/ConvertTranscriptFile_SamToCsv.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
line wrap: on
line source

<tool id="ConvertTranscriptFile_SamToCsv" name="Sam -> Csv">
  <description>Convert Sam File to Csv File.</description>
  <command interpreter="python"> ../Java/Python/ -i $inputFile -f sam -o $outputFile -g csv yes 2>$logFile </command>
    <param name="inputFile" type="data" label="Input File" format="sam"/>

    <data format="csv" name="outputFile" label="[sam -> csv] Output File"/>
    <data format="txt" name="logFile" label="[sam -> csv] Log File"/>