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view picard_FixMateInformation.xml @ 5:3d4f1fa26f0e draft
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author | devteam |
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date | Tue, 16 Dec 2014 19:03:21 -0500 |
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children | 3a3234d7a2e8 |
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<tool name="FixMateInformation" id="picard_FixMateInformation" version="1.126.0"> <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> <requirements> <requirement type="package" version="1.126.0">picard</requirement> </requirements> <macros> <import>picard_macros.xml</import> </macros> <command> @java_options@ java -jar \$JAVA_JAR_PATH/picard.jar FixMateInformation INPUT="${inputFile}" OUTPUT="${outFile}" ASSUME_SORTED=${assume_sorted} ADD_MATE_CIGAR=${add_mate_cigar} SORT_ORDER=coordinate VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR </command> <inputs> <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> <expand macro="VS" /> </inputs> <outputs> <data format="bam" name="outFile" label="${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="2"/> </test> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <help> **Purpose** Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged. ------ .. class:: warningmark **Warning on using ASSUME_SORTED option** Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb is to assume that the BAM you are working with is coordinate sorted. @dataset_collections@ @description@ ASSUME_SORTED=Boolean AS=Boolean If true, assume that the input file is queryname sorted, even if the header says otherwise. Default value: false. ADD_MATE_CIGAR=Boolean MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. @more_info@ </help> </tool>