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annotate picard_ReplaceSamHeader.xml @ 21:1181366ba593 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author iuc
date Mon, 17 Feb 2020 15:23:48 +0000
parents a5a13ea16d17
children 4740a2548206
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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}" "${fasta_file}" &&
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16 picard
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17 ReplaceSamHeader
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19 INPUT='$escaped_element_identifier'
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20 HEADER="${header}"
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21 OUTPUT="${outFile}"
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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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58
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59 </help>
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60 <expand macro="citations" />
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61 </tool>