comparison correct_barcodes.xml @ 27:f33b89fe9f82 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'e513259f9701a68e53baddaeedfa51406df857bf\n'-dirty

26:a2dc1e1c10db

  <description>of duplex sequencing reads</description>
  <requirements>
    <requirement type="package" version="2.1.0">bowtie2</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="1.9">networkx</requirement>
    <requirement type="package" version="0.6">duplex</requirement>
    <requirement type="set_environment">DUPLEX_DIR</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <command detect_errors="exit_code">bash "\$DUPLEX_DIR/baralign.sh" '$input' refdir barcodes.bam
    &amp;&amp; samtools view -f 256 barcodes.bam
    | python "\$DUPLEX_DIR/correct.py" -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa
    | sort &gt; '$output'
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
    <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/>
    <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/>

27:f33b89fe9f82

  <description>of duplex sequencing reads</description>
  <requirements>
    <requirement type="package" version="2.1.0">bowtie2</requirement>
    <requirement type="package" version="0.1.18">samtools</requirement>
    <requirement type="package" version="1.9">networkx</requirement>
    <requirement type="package" version="0.6.1">duplex</requirement>
    <!-- TODO: require Python 2.7 -->
  </requirements>
  <command detect_errors="exit_code">correct-barcodes.sh -d $dist -m $mapq -p $pos '$input' &gt; '$output'
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
    <param name="dist" type="integer" value="1" min="1" label="Maximum edit distance" help="Only use alignments where the barcodes differ by at most these many errors."/>
    <param name="mapq" type="integer" value="20" min="0" label="Minimum mapping quality" help="Only use alignments whose MAPQ is at least this."/>