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annotate SMART/DiffExpAnal/bam_to_sam_parallel.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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1 <tool id="bam_to_sam_parallel" name="BAM to SAM (for DEA)" version="1.0.0">
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2 <description>converts a list of BAM format files to SAM format.</description>
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3 <requirements>
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4 <requirement type="package">samtools</requirement>
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5 </requirements>
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6 <command interpreter="python"> bam_to_sam_parallel.py
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7 --input1=$input1
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8 --output1=$output1
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9 $header
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10 $tar $outputTarFile
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11 </command>
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12 <inputs>
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13 <param name="input1" type="data" format="txt" label="BAM File LIST to Convert" />
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14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
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15 <param name="tar" type="boolean" truevalue="-t" falsevalue="" checked="false" label="tar option" help="This option creates a tar file for all out results." />
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="output1" label="converted SAM LIST files " />
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19 <data name="outputTarFile" format="tar">
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20 <filter>tar</filter>
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21 </data>
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22 </outputs>
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23 <help>
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24
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25 **What it does**
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26
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27 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
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28
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29 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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30
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31 </help>
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32 </tool>