comparison bwa-mem.xml @ 15:4d82cf59895e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit dead2eaab58698fe02b8bb068f8d859eba551e8d

14:051eba708f43

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>

        ${analysis_type.io_options.a}
        ${analysis_type.io_options.C}
        ${analysis_type.io_options.V}
        ${analysis_type.io_options.Y}
        ${analysis_type.io_options.M}
      #end if

    #end if

    ## Handle read group options...

          <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
            <option value="set">Set</option>
            <option value="do_not_set" selected="True">Do not set</option>
          </param>
          <when value="set">
            <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
            <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
            <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
            <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
            <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>

15:4d82cf59895e

<?xml version="1.0"?>
<tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.0">
  <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
  <macros>
    <import>read_group_macros.xml</import>
    <import>bwa_macros.xml</import>
  </macros>

        ${analysis_type.io_options.a}
        ${analysis_type.io_options.C}
        ${analysis_type.io_options.V}
        ${analysis_type.io_options.Y}
        ${analysis_type.io_options.M}
        ${analysis_type.io_options.five}
      #end if

    #end if

    ## Handle read group options...

          <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
            <option value="set">Set</option>
            <option value="do_not_set" selected="True">Do not set</option>
          </param>
          <when value="set">
            <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
            <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
            <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
            <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
            <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
            <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>