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annotate picard_ReplaceSamHeader.xml @ 30:b502c227b5e6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c
author iuc
date Mon, 22 Aug 2022 09:56:00 +0000
parents 881d7645d1bf
children f9242e01365a
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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 <xrefs>
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8 <xref type="bio.tools">picard_replacesamheader</xref>
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9 </xrefs>
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10 <expand macro="requirements" />
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11 <command detect_errors="exit_code"><![CDATA[
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12 @java_options@
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13 @symlink_element_identifier@
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15 ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
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16 #set $fasta_file="local_fasta.fa"
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17 ln -s "${inputFile}" "${fasta_file}" &&
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19 picard
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20 ReplaceSamHeader
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22 INPUT='$escaped_element_identifier'
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23 HEADER="${header}"
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24 OUTPUT="${outFile}"
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26 QUIET=true
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27 VERBOSITY=ERROR
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28 @TMPDIR_OPTION@
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30 ]]></command>
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31 <inputs>
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32 <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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33 <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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34 </inputs>
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35
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36 <outputs>
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37 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
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38 </outputs>
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39
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40 <tests>
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41 <test>
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42 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
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43 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
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44 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
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45 </test>
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46 </tests>
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48
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49 <help>
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50
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51 **Purpose**
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52
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53 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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54 @dataset_collections@
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55
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56 @description@
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57
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58 HEADER=File SAM file from which SAMFileHeader will be read. Required.
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59
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60 @more_info@
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62 </help>
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63 <expand macro="citations" />
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64 </tool>