comparison picard_DownsampleSam.xml @ 7:08f69add4d06 draft

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

6:961236c5ec73

  <description>Downsample a file to retain a subset of the reads</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
    @java_options@
    java -jar
    \$JAVA_JAR_PATH/picard.jar
    DownsampleSam
      INPUT="${inputFile}"
      OUTPUT="${outFile}"
      PROBABILITY=${probability}
      RANDOM_SEED=${seed}
      QUIET=true
      VERBOSITY=ERROR
      VALIDATION_STRINGENCY=${validation_stringency}
  </command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
    <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
    <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
    
    <expand macro="VS" />
    
  </inputs>
  
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
  </outputs>
  

7:08f69add4d06

  <description>Downsample a file to retain a subset of the reads</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    picard
    DownsampleSam
      INPUT="${inputFile}"
      OUTPUT="${outFile}"
      PROBABILITY=${probability}
      RANDOM_SEED=${seed}
      QUIET=true
      VERBOSITY=ERROR
      VALIDATION_STRINGENCY=${validation_stringency}
  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
    <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
    <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
    
    <expand macro="VS" />
    
  </inputs>
  
  
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
  </outputs>