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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:31:14 +0000
parents e65f2d5fd3d8
children
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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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29 ]]></command>
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30 <inputs>
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31 <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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32 <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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33 </inputs>
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34
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35 <outputs>
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36 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
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42 <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
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43 <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
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44 </test>
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45 </tests>
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47
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48 <help>
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49
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50 **Purpose**
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51
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52 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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53 @dataset_collections@
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54
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55 @description@
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56
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57 HEADER=File SAM file from which SAMFileHeader will be read. Required.
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58
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59 @more_info@
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61 </help>
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62 <expand macro="citations" />
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63 </tool>