comparison picard_FixMateInformation.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

6:961236c5ec73

  <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>
  </macros>
  <expand macro="requirements" />
  <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"/>
 

    <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**

7:08f69add4d06

  <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>
  </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}

    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"/>
 

    <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**