view seqtk_trimfq.xml @ 0:e0a0fd938de4 draft

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<?xml version="1.0"?>
<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
  <description>trim FASTQ using the Phred algorithm</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[seqtk trimfq
#if $mode.mode_select == "quality":
-q $mode.q
-l $mode.l
#else:
-b $mode.b
-e $mode.e
#end if
$in_file
> $default]]></command>
  <inputs>
    <expand macro="in_faq"/>
    <conditional name="mode">
        <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
            <option value="quality">Quality</option>
            <option value="position">Length/Position</option>
        </param>
        <when value="quality">
            <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/>
            <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/>
        </when>
        <when value="position">
            <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/>
            <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/>
        </when>
    </conditional>
  </inputs>
  <outputs>
    <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/>
  </outputs>
  <tests>
    <test>
      <param name="in_file" value="seqtk_trimfq.fq"/>
      <param name="mode_select" value="quality"/>
      <param name="q" value="0.05"/>
      <param name="l" value="30"/>
      <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
    </test>
    <test>
      <param name="in_file" value="seqtk_trimfq.fq"/>
      <param name="mode_select" value="position"/>
      <param name="b" value="5"/>
      <param name="e" value="5"/>
      <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Trim a fastq file based on Phred scores, or by length

@ATTRIBUTION@
]]></help>
</tool>