annotate fq2fa.xml @ 2:edda44d54b59 draft default tip

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<tool id="fq2fa" name="fq2fa" version="1.1.1 (Oct 18, 2012)">
  <description>fq2fa is a simple tool given by IDBA package that allows to convert fastq to fasta, merge paired-end reads and filter out reads containing 'N's</description>
  <command>
    fq2fa
    #if $fileLayout.layout=='paired'
      --paired $fileLayout.sequence
    #else if $fileLayout.layout=='merge'
      --merge $fileLayout.sequenceR1 $fileLayout.sequenceR2
    #else
      $fileLayout.sequence
    #end if
    $filter
    $output
  </command>
  <inputs>
    <conditional name="fileLayout">
      <param name="layout" type="select" label="File layout">
        <option value="">single end</option>
        <option value="paired">paired-end in one file</option>
        <option value="merge">paired-end in two files</option>
      </param>
      <when value="">
        <param name="sequence" type="data" format="fastq" label="Single sequence file"/>
      </when>
      <when value="--paired">
        <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/>
      </when>
      <when value="--merge">
        <param name="sequenceR1" type="data" format="fastq" label="Forward sequence file (R1)"/>
        <param name="sequenceR2" type="data" format="fastq" label="Reverse sequence file (R2)"/>
      </when>
    </conditional>
    <param name="filter" type="boolean" checked="false" truevalue="--filter" falsevalue="" label="Filter out reads containing 'N'"/>
  </inputs>
  <outputs>
		<data name="output" format="fasta" label="Fasta from fq2fa"/>
	</outputs>
  <help>
=====
fq2fa
=====
Convert Fastq sequences to Fasta sequences.

| ``Usage:``
| ``fq2fa tmp.fq tmp.fa [...]``
| ``fq2fa --paired tmp.fq tmp.fa``
| ``fq2fa --merge tmp_1.fq tmp_2.fq tmp.fa``
|
| Allowed Options:

--paired  if the reads are paired-end in one file
--merge   if the reads are paired-end in two files
--filter  filter out reads containing 'N'
  </help>
</tool>