comparison picard_DownsampleSam.xml @ 143:b2ca2d181fb4 draft

fixed downsample sam in picard1106 (accept bam)

142:844fa42ad305

<tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0">
    <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
   <description>Down-sample a file to retain a subset of the reads</description>
   <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input=$inputFile
      --output=$outFile
      --probability=$probability
      --seed=$seed
      -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
  </command>
  <inputs>
    <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled"
           help="If empty, upload or import a SAM dataset." />
    <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
    <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
  </inputs>
  <outputs>
    <data name="outFile" format="sam" label="${tool.name} on ${on_string}">
    </data>
  </outputs>
  <tests>
    <test>
      <param name="inputFile" value="cleansamtestinput.sam" />
      <param name="probability" value="0.1" />
      <param name="seed" value="2" />
      <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
    </test>
  </tests>
  <help>

143:b2ca2d181fb4

<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.106.0">
    <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
   <description>Down-sample a file to retain a subset of the reads</description>
   <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input "$inputFile"
      --output "$outFile"
      --probability=$probability
      --output-format $outputFormat
      --seed=$seed
      -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
  </command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset to be downsampled"
           help="If empty, upload or import a SAM or BAM dataset." />
    <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
    <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled ${outputFormat}">
      <change_format>
        <when input="outputFormat" value="sam" format="sam" />
      </change_format>
    </data>
  </outputs>
 
  <tests>
    <test>
      <param name="inputFile" value="cleansamtestinput.sam"  ftype="sam" />
      <param name="probability" value="0.1" />
      <param name="seed" value="2" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
    </test>
  </tests>
  <help>