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annotate picard_ReplaceSamHeader.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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1 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.0">
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2 <description>replace header in a SAM/BAM dataset</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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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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11 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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12 #set $fasta_file="local_fasta.fa"
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13 ln -s "${inputFile}" "${fasta_file}" &&
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15 picard
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16 ReplaceSamHeader
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18 INPUT="${inputFile}"
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19 HEADER="${header}"
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20 OUTPUT="${outFile}"
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22 QUIET=true
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23 VERBOSITY=ERROR
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25 ]]></command>
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26 <inputs>
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27 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
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28 <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
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29 </inputs>
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31 <outputs>
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32 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
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33 </outputs>
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35 <tests>
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36 <test>
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37 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
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38 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
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39 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
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40 </test>
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41 </tests>
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44 <help>
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46 **Purpose**
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48 Replace the SAMFileHeader in a SAM/BAM dataset with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input datasets must be the same.
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49 @dataset_collections@
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51 @description@
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53 HEADER=File SAM file from which SAMFileHeader will be read. Required.
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55 @more_info@
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57 </help>
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58 </tool>
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