comparison picard_MergeBamAlignment.xml @ 31:585027e65f3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

30:b502c227b5e6

<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>merge alignment data with additional info stored in an unmapped BAM dataset</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@
    #set $picard_dict = "localref.dict"

    <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
    <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
    <expand macro="VS" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with merged alignments"/>
  </outputs>
  <tests>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" />

      <param name="is_bisulfite_sequence" value="False"/>
      <param name="aligned_reads_only" value="False"/>
      <param name="max_insertions_or_deletions" value="1"/>
      <param name="read1_trim" value="0"/>
      <param name="read2_trim" value="0"/>
      <param name="orientation" value="FR"/>
      <param name="aligner_proper_pair_flags" value="False"/>
      <param name="primary_alignment_strategy" value="BestMapq"/>
      <param name="clip_overlapping_reads" value="True"/>
      <param name="include_secondary_alignments" value="True"/>
      <param name="add_mate_cigar" value="True"/>

31:585027e65f3b

<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">2</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    #set $picard_dict = "localref.dict"

    <param name="include_secondary_alignments" type="boolean" checked="True" label="If false, do not write secondary alignments to output" help="INCLUDE_SECONDARY_ALIGNMENTS; default=True"/>
    <param name="add_mate_cigar" type="boolean" checked="True" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
    <expand macro="VS" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM"/>
  </outputs>
  <tests>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" value="picard_MergeBamAlignment_ref.fa" ftype="fasta" />

      <param name="is_bisulfite_sequence" value="False"/>
      <param name="aligned_reads_only" value="False"/>
      <param name="max_insertions_or_deletions" value="1"/>
      <param name="read1_trim" value="0"/>
      <param name="read2_trim" value="0"/>
      <param name="orientations" value="FR"/>
      <param name="aligner_proper_pair_flags" value="False"/>
      <param name="primary_alignment_strategy" value="BestMapq"/>
      <param name="clip_overlapping_reads" value="True"/>
      <param name="include_secondary_alignments" value="True"/>
      <param name="add_mate_cigar" value="True"/>