comparison picard_DownsampleSam.xml @ 20:2a17c789e0a5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a

19:5053a18d9bc8

<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>Downsample a file to retain a subset of the reads</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">0</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

      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" />

20:2a17c789e0a5

<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>Downsample a file to retain a subset of the reads</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

      OUTPUT="${outFile}"
      PROBABILITY=${probability}
      RANDOM_SEED=${seed}
      QUIET=true
      VERBOSITY=ERROR
      @TMPDIR_OPTION@
      VALIDATION_STRINGENCY=${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" />