Mercurial > repos > devteam > picard
diff picard_ReplaceSamHeader.xml @ 33:3f254c5ced1d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
| author | iuc |
|---|---|
| date | Sun, 03 Mar 2024 16:06:11 +0000 |
| parents | f9242e01365a |
| children |
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--- a/picard_ReplaceSamHeader.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ReplaceSamHeader.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,51 +1,46 @@ -<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> +<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> <description>replace header in a SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">0</token> </macros> <xrefs> <xref type="bio.tools">picard_replacesamheader</xref> </xrefs> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @java_options@ @symlink_element_identifier@ ## Two lines below are due to the fact that picard likes fasta files to have extension .fa #set $fasta_file="local_fasta.fa" - ln -s "${inputFile}" "${fasta_file}" && + ln -sf '${inputFile}' '${fasta_file}' && - picard - ReplaceSamHeader + picard ReplaceSamHeader - INPUT='$escaped_element_identifier' - HEADER="${header}" - OUTPUT="${outFile}" + --INPUT '$escaped_element_identifier' + --HEADER '${header}' + --OUTPUT '${outFile}' - QUIET=true - VERBOSITY=ERROR + --QUIET true + --VERBOSITY ERROR ]]></command> - <inputs> - <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/> - <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/> - </inputs> - - <outputs> - <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/> - <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/> - <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/> - </test> - </tests> - - - <help> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/> + </inputs> + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/> + <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/> + <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/> + </test> + </tests> + <help> **Purpose** @@ -59,5 +54,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>