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annotate picard_ReplaceSamHeader.xml @ 12:a459ead5ab75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author iuc
date Thu, 13 Apr 2017 19:09:04 -0400
parents 41b8d087a2d2
children 486d7500da69
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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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9 @symlink_element_identifier@
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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}" "${fasta_file}" &&
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15 picard
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16 ReplaceSamHeader
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18 INPUT='$escaped_element_identifier'
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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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43
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44 <help>
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45
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46 **Purpose**
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47
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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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