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annotate picard_ReplaceSamHeader.xml @ 24:b9fbec5ac6b2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author iuc
date Fri, 31 May 2019 03:21:52 -0400
parents 2a17c789e0a5
children 881d7645d1bf
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1 <tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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 <token name="@WRAPPER_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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12 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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13 #set $fasta_file="local_fasta.fa"
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14 ln -s "${inputFile}" "${fasta_file}" &&
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
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16 picard
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17 ReplaceSamHeader
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19 INPUT='$escaped_element_identifier'
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20 HEADER="${header}"
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21 OUTPUT="${outFile}"
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22
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23 QUIET=true
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24 VERBOSITY=ERROR
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25 @TMPDIR_OPTION@
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27 ]]></command>
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28 <inputs>
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29 <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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30 <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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31 </inputs>
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32
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33 <outputs>
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34 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
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40 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
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41 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
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42 </test>
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43 </tests>
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45
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46 <help>
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47
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48 **Purpose**
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49
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50 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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51 @dataset_collections@
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52
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53 @description@
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54
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55 HEADER=File SAM file from which SAMFileHeader will be read. Required.
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56
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57 @more_info@
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59 </help>
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60 <expand macro="citations" />
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61 </tool>