comparison precheck.xml @ 29:9d28b4509c02 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'17e6160270d30b519b08f4d0701e0c2ad3adbb57\n'-dirty

28:0c3e8fa84c38

<?xml version="1.0"?>
<tool id="precheck" name="Du Novo: Check input" version="2.14">
  <requirements>
    <requirement type="package" version="2.14">dunovo</requirement>
  </requirements>
  <description>for family content</description>
  <command detect_errors="exit_code">
    precheck.py $validate --tag-length $tag_len --constant-length $const_len --min-reads $min_reads
      $fastq1 $fastq2 &gt; $output
  </command>
  <inputs>
    <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
    <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/>
    <param name="min_reads" type="integer" value="3" min="0" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
    <param name="tag_len" type="integer" value="12" min="0" label="Tag length" help="Length of each random barcode on the ends of the fragments."/>
    <param name="const_len" type="integer" value="5" min="0" label="Invariant sequence length" help="Length of the sequence between the tag and actual sample sequence (the restriction site, normally)."/>
    <param name="validate" type="boolean" truevalue="--validate" falsevalue="" checked="False" label="Check read names" help="Make sure the names of the reads in each pair is the same. If checked, this will fail if there is a mismatch."/>
  </inputs>
  <outputs>
    <data name="output" format="tabular"/>
  </outputs>

29:9d28b4509c02

<?xml version="1.0"?>
<tool id="precheck" name="Du Novo: Check input" version="2.15">
  <requirements>
    <requirement type="package" version="2.15">dunovo</requirement>
  </requirements>
  <description>for family content</description>
  <command detect_errors="exit_code">
    precheck.py $check_ids --tag-length $tag_len --constant-length $const_len --min-reads $min_reads
      '$fastq1' '$fastq2' &gt; '$output'
  </command>
  <inputs>
    <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/>
    <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/>
    <param name="min_reads" type="integer" value="3" min="0" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
    <param name="tag_len" type="integer" value="12" min="0" label="Tag length" help="Length of each random barcode on the ends of the fragments."/>
    <param name="const_len" type="integer" value="5" min="0" label="Invariant sequence length" help="Length of the sequence between the tag and actual sample sequence (the restriction site, normally)."/>
    <param name="check_ids" type="boolean" truevalue="--validate" falsevalue="--no-check-ids" checked="True" label="Check read names" help="Make sure the ids of the reads in each pair is the same. If checked, this will fail if there is a mismatch."/>
  </inputs>
  <outputs>
    <data name="output" format="tabular"/>
  </outputs>