view tools/ilmn_pacbio/abyss.xml @ 0:9071e359b9a3

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<tool id="abyss" name="ABySS" version="1.0.0">
  <description>Short-read de Bruijn assembly</description>
  <command interpreter="python">
    quake_wrapper.py -k $k -r $input1 -p 8 > $output1
  </command>
  <inputs>
    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
  </inputs>
  <outputs>
    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
  </outputs>
  <help>

**What it does**

TBD.  Calls ABySS assembler

**Parameter list**

k

**Output**

Corrected reads

  </help>
</tool>