comparison dunovo.xml @ 9:fa563fa9b330 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'74b84167148cb0a0d7c6ac83123e8c957f85fe37\n'-dirty

8:658eefb99fd7

<?xml version="1.0"?>
<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.12">
  <description>from duplex sequencing alignments</description>
  <requirements>
    <requirement type="package" version="2.0.12">dunovo</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <version_command>make-consensi.py --version</version_command>
  <command detect_errors="exit_code">
    make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'

      --sscs1 '$sscs1' --sscs2 '$sscs2'
    #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Aligned input reads" />
    <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
    <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or &quot;N&quot; will be used."/>
    <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="If no base at the position appears in at least this many reads, &quot;N&quot; will be used."/>
    <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
    <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
      <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>

9:fa563fa9b330

<?xml version="1.0"?>
<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.14">
  <description>from duplex sequencing alignments</description>
  <requirements>
    <requirement type="package" version="2.14">dunovo</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <version_command>make-consensi.py --version</version_command>
  <command detect_errors="exit_code">
    make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2'

      --sscs1 '$sscs1' --sscs2 '$sscs2'
    #end if
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Aligned input reads" />
    <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads for a consensus" help="This many reads are necessary to form a single-strand consensus sequence. Families smaller than this will be skipped."/>
    <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or &quot;N&quot; will be used."/>
    <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="If no base at the position appears in at least this many reads, &quot;N&quot; will be used."/>
    <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
    <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
      <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>