Mercurial > repos > devteam > picard
diff picard_FixMateInformation.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_FixMateInformation.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_FixMateInformation.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,50 +1,43 @@ -<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">1</token> - </macros> - <expand macro="requirements" /> - <command detect_errors="exit_code"><![CDATA[ +<tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ @java_options@ - picard - FixMateInformation - INPUT="${inputFile}" - OUTPUT="${outFile}" - ASSUME_SORTED=${assume_sorted} - ADD_MATE_CIGAR=${add_mate_cigar} + picard FixMateInformation + --INPUT '${inputFile}' + --OUTPUT '${outFile}' + --ASSUME_SORTED ${assume_sorted} + --ADD_MATE_CIGAR ${add_mate_cigar} - SORT_ORDER=coordinate - VALIDATION_STRINGENCY="${validation_stringency}" - QUIET=true - VERBOSITY=ERROR + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]></command> - <inputs> - <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> - <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> - <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> - - <expand macro="VS" /> - - </inputs> - - <outputs> - <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> - <param name="add_mate_cigar" value="True"/> - <param name="assume_sorted" value="False"/> - <param name="validation_stringency" value="LENIENT"/> - <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/> - </test> - </tests> - - - <help> + <inputs> + <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> + <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> + <expand macro="VS"/> + </inputs> + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> + <param name="add_mate_cigar" value="True"/> + <param name="assume_sorted" value="False"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/> + </test> + </tests> + <help> **Purpose** @@ -73,5 +66,5 @@ @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>