comparison dunovo.xml @ 3:00dde366870a draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n'

2:a9cb6fb9ea94

<?xml version="1.0"?>
<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6">
  <description>from duplex sequencing alignments</description>
  <requirements>
    <requirement type="package" version="0.7.6">dunovo</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input'
    #if $keep_sscs:
      --sscs-file sscs.fa
    #end if
    > duplex.fa
    && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2'
    #if $keep_sscs:
      && outconv.py sscs.fa -1 '$sscs1' -2 '$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="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>
      <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
    </param>

    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="families.msa.tsv"/>
      <output name="dcs1" file="families.cons_1.fa"/>
      <output name="dcs2" file="families.cons_2.fa"/>
    </test>
  </tests>
  <citations>
    <citation type="bibtex">@article{Stoler2016,
      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},

3:00dde366870a

<?xml version="1.0"?>
<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.8.1">
  <description>from duplex sequencing alignments</description>
  <requirements>
    <requirement type="package" version="0.8.1">dunovo</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <command detect_errors="exit_code">
    dunovo.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'
    #if $keep_sscs:
      --sscs1 '$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="The threshold to use when making consensus sequences. 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="The minimum number of reads a base must appear in to be used as the consensus base. 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>
      <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
    </param>

    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="families.msa.tsv"/>
      <output name="dcs1" file="families.dcs_1.fa"/>
      <output name="dcs2" file="families.dcs_2.fa"/>
    </test>
  </tests>
  <citations>
    <citation type="bibtex">@article{Stoler2016,
      author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton},