comparison picard_ReorderSam.xml @ 2:9227b8c3093b

Updated command line format per dev team standards.

1:e0232cbac965

<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input=$inputFile
      #if $source.indexSource == "built-in"
        --ref="${source.ref.fields.path}"
      #else
        --ref-file=$refFile
        --species-name=$source.speciesName
        --build-name=$source.buildName
        --trunc-names=$source.truncateSeqNames
      #end if
      --allow-inc-dict-concord=$allowIncDictConcord
      --allow-contig-len-discord=$allowContigLenDiscord
      --output-format=$outputFormat
      --output=$outFile
      --tmpdir "${__new_file_path__}" 
      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"

2:9227b8c3093b

<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input="${inputFile}"
      #if $source.indexSource == "built-in"
        --ref="${source.ref.fields.path}"
      #else
        --ref-file="${refFile}"
        --species-name="${source.speciesName}"
        --build-name="${source.buildName}"
        --trunc-names="${source.truncateSeqNames}"
      #end if
      --allow-inc-dict-concord="${allowIncDictConcord}"
      --allow-contig-len-discord="${allowContigLenDiscord}"
      --output-format="${outputFormat}"
      --output="${outFile}"
      --tmpdir "${__new_file_path__}" 
      -j "\$JAVA_JAR_PATH/ReorderSam.jar"
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"