comparison picard_CleanSam.xml @ 7:08f69add4d06 draft

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

6:961236c5ec73

  <description>perform SAM/BAM grooming</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    java -jar \$JAVA_JAR_PATH/picard.jar
    CleanSam
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${validation_stringency}
  </command>
  
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    
    <expand macro="VS" />

  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
    </data>
  </outputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />

7:08f69add4d06

  <description>perform SAM/BAM grooming</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    picard
    CleanSam
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    QUIET=true
    VERBOSITY=ERROR
    VALIDATION_STRINGENCY=${validation_stringency}
  ]]></command>
  
  <inputs>
    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    
    <expand macro="VS" />

  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
    </data>
  </outputs>
  
  
  <tests>
    <test>
      <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
      <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />