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annotate picard_CleanSam.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
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52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.0">
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2 <description>perform SAM/BAM grooming</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 picard
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10 CleanSam
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11 INPUT="${inputFile}"
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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12 OUTPUT="${outFile}"
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 QUIET=true
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14 VERBOSITY=ERROR
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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15 VALIDATION_STRINGENCY=${validation_stringency}
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08f69add4d06 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
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16 ]]></command>
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18 <inputs>
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19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 <expand macro="VS" />
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23 </inputs>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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25 <outputs>
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26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 </data>
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 </outputs>
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31 <tests>
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32 <test>
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33 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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34 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
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35 </test>
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36 </tests>
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38 <help>
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40 .. class:: infomark
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42 **Purpose**
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44 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
52fdfc45590a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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46 1. to soft-clip an alignment that hangs off the end of its reference sequence.
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47 2. to set MAPQ to 0 if a read is unmapped.
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49 @dataset_collections@
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51 @more_info@
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53 </help>
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54 </tool>