comparison picard_ReorderSam.xml @ 15:a5a13ea16d17 draft

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

14:486d7500da69

<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>reorder reads to match ordering in reference sequences</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@

    #if str( $reference_source.reference_source_selector ) == "history":

      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR

      &&

    #else:

      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"

      VALIDATION_STRINGENCY="${validation_stringency}"
      QUIET=true
      VERBOSITY=ERROR

  ]]></command>

  <inputs>

15:a5a13ea16d17

<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>reorder reads to match ordering in reference sequences</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@

    #if str( $reference_source.reference_source_selector ) == "history":

      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR
      @TMPDIR_OPTION@

      &&

    #else:

      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"

      VALIDATION_STRINGENCY="${validation_stringency}"
      QUIET=true
      VERBOSITY=ERROR
      @TMPDIR_OPTION@

  ]]></command>

  <inputs>