view trimmer.xml @ 0:c824894e0827 draft

planemo upload commit bb6c51fa3c8501e779f3b266d17f4900d98fc431-dirty

<tool id="sequence_content_trimmer" version="0.1" name="Sequence Content Trimmer">
  <description>trim reads based on certain bases</description>
  <command interpreter="python">
  trimmer.py $input1
  #if $paired.is_paired:
    $input2 $output1 $output2
    #if ('fasta' in $input1.extension and 'fastq' in $input2.extension) or ('fastq' in $input1.extension and 'fasta' in $input2.extension)
      --error 'Both input files must be either fastq or fasta (no mixing the two).'
    #end if
  #end if
  #if $input1.extension == 'fastq' or $input1.extension == 'fastqsanger' or $input1.extension == 'fastqillumina' or $input1.extension == 'fastqsolexa'
    -f fastq
  #elif $input1.extension == 'fasta'
    -f fasta
  #else
    -f $input1.extension
  #end if
  -b $bases -t $thres -w $win_len $invert
  #if $min_len.has_min_len:
    -m $min_len.value
  #end if
  #if not $paired.is_paired:
    &gt; $output1
  #end if
  </command>
  <inputs>
    <conditional name="paired">
      <param name="is_paired" type="select" label="Paired reads?">
        <option value="" selected="True">Unpaired</option>
        <option value="true">Paired</option>
      </param>
      <when value="true">
        <param name="input1" type="data" format="fasta,fastq" label="Input reads (mate 1)"/>
        <param name="input2" type="data" format="fasta,fastq" label="Input reads (mate 2)"/>
      </when>
      <when value="">
        <param name="input1" type="data" format="fasta,fastq" label="Input reads"/>
      </when>
    </conditional>
    <param name="bases" type="text" value="N" label="Bases to filter on"/>
    <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
    <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/>
    <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the &quot;filter bases&quot; list exceeds the threshold."/>
    <conditional name="min_len">
      <param name="has_min_len" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set a minimum read length"/>
      <when value="true"> 
        <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output1" format_source="input1"/>
    <data name="output2" format_source="input2">
      <filter>paired['is_paired']</filter>
    </data>
  </outputs>

  <help>

.. class:: infomark

**What it does**

This tool trims the 3' ends of reads based on the presence of the given bases. For instance, trim when N's are encountered or when the GC content exceeds a certain frequency.


.. class:: infomark

**Input**

The inputs can be in the following formats: fasta, fastq, fastqsanger, fastqillumina, and fastqsolexa. Both must be either a fasta or fastq type (no mixing fastq and fasta).

  </help>

</tool>