/tools/ilmn_pacbio/smrtpipe_filter.xml

<tool id="smrtpipe_filter" name="SMRTpipe Filter" version="1.0.0">
  <description>Produce filtered reads from a set of PacBio primary analysis outputs.</description>
  <command interpreter="python">
    smrtpipe_galaxy.py --output=data/filtered_subreads.fasta --galaxy_output=${outfile} ${iniFile}
  </command>
  <inputs>
    <conditional name="source">
      <param name="input_source" type="select" label="Choose the source for the analysis inputs">
        <option value="path">Path to fofn or multiple bas.h5 paths</option>
        <option value="history">History</option>
      </param>
      <when value="path">
        <repeat name="inputFiles" title="Input files">
          <param name="path" type="text" label="File path" size="75"/>
        </repeat>
      </when>
      <when value="history">
        <param name="input1" type="data" format="tabular" label="File containing input paths" />
      </when>
    </conditional>
    <param name="minimum_readlength" type="integer" value="50" label="Minimum raw readlength" />
    <param name="minimum_readscore" type="float" value="0.75" label="Minimum read quality" />
  </inputs>
  <configfiles>
    <configfile name="iniFile">
[input]
#if $source.input_source=="history":
#for $l in open($source.input1.file_name,'r'):
$l
#end for
#else
#for $p in $source.inputFiles
${p.path}
#end for
#end if

[S_Filter]
filters=MinRL=${minimum_readlength},MinReadScore=${minimum_readscore}
    </configfile>
  </configfiles>
  <outputs>
    <data name="outfile" format="fasta" label="Filtered subreads" />
  </outputs>
  <help>

**What it does**

Filters PacBio bas.h5 files and produces a FASTA file of filtered subreads.

In PacBio SMRT sequencing, the template format is a SMRTbell: a circular
molecule with adapters at two locations in the circle.  The subreads are the
portions of the read between adapters.

**Parameter list**

Minimum readlength
    Only keep reads from ZMWs that produced this many bases or more.

Minimum read quality
    Only keep reads with overall quality scores of this value or more.  The read quality score is a *de novo* prediction of the accuracy of the read.

**Output**

FASTA file of filtered reads.

  </help>
</tool>