comparison picard_AddOrReplaceReadGroups.xml @ 7:08f69add4d06 draft

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

6:961236c5ec73

  <macros>
    <import>picard_macros.xml</import>
    <import>read_group_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @define_read_group_helpers@
    #set $rg_auto_name = $read_group_name_default($inputFile)
    @set_read_group_vars@
    @java_options@
    java -jar \$JAVA_JAR_PATH/picard.jar
      AddOrReplaceReadGroups
      INPUT="${inputFile}"
      $format_read_group("RGLB=", $rg_lb, '"')
      $format_read_group("RGPL=", $rg_pl, '"')
      $format_read_group("RGPU=", $rg_pu, '"')

  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
  </outputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <tests>
    <test>
      <param name="inputFile" value="picard_ARRG.bam" />
      <param name="LB" value="tumor-a" />

7:08f69add4d06

  <macros>
    <import>picard_macros.xml</import>
    <import>read_group_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code">
    @define_read_group_helpers@
    #set $rg_auto_name = $read_group_name_default($inputFile)
    @set_read_group_vars@
    @java_options@
    picard
      AddOrReplaceReadGroups
      INPUT="${inputFile}"
      $format_read_group("RGLB=", $rg_lb, '"')
      $format_read_group("RGPL=", $rg_pl, '"')
      $format_read_group("RGPU=", $rg_pu, '"')

  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
  </outputs>
  
  
  <tests>
    <test>
      <param name="inputFile" value="picard_ARRG.bam" />
      <param name="LB" value="tumor-a" />