view fixFastq.xml @ 3:950609434f7a draft

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<tool id="fixFastq" name="Fix barcodes" version="1.0.0">
  <description> generated using Hamming encoding</description>
  <command interpreter="python">fixFastq.py $strict $list $fastq $out</command>
  <inputs>
    <param format="text" name="strict" type="select" value=""/>
      <label>Replace unknown barcodes with N</label>
      <option value="">No</option>
      <option value="-s">Yes</option>
    <param format="tabular" name="list" type="data" label="List of barcodes used"/>
    <param format="fastqsanger" name="fastq" type="data" label="Barcoded reads"/>
  </inputs>
  <outputs>
    <data format="fastqsanger" name="out"/>
  </outputs>
  <stdio>
    <exit_code range="127" level="fatal" description="Cannot find fixFastq.py"/>
  </stdio>
  <requirements>
    <requirement type="package" version="1.0">hamstring</requirement>
  </requirements>
  <help>
    This program accepts a fastqsanger file containing reads that are barcoded on the 5' end using a Hamming7,4 DNA barcode. A list of valid barcodes is checked, 
    and if the barcode checksum fails the barcode is corrected and checked against this list. If the barcode is not present in the list, it may be replaced 
    with 'N' to denote ambiguity.
  </help>
</tool>