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<?xml version="1.0"?>
<tool id="ucsc_pslcdnafilter" name="UCSC pslCDnaFilter" version="1.0">
    <description>Filter cDNA alignments in psl format</description>
    <requirements>
      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      pslReps -minAli=0.25 '${alignment}' output.reps.psl output.reps.psr
      && faPolyASizes '${query}' query.polyA
      && pslCDnaFilter
            #if $assembly_type == "native"
                  -localNearBest=0.001
                  #if $assembly_category == "finished"
                        -minId=0.95
                        -minCover=0.25
                  #elif $assembly_category == "well-ordered"
                        -minId=0.95
                        -minCover=0.15
                  #else
                        -minId=0.94
                        -minAlnSize=80
                  #end if
            #else
                  -localNearBest=0.010
                  #if $assembly_category == "finished"
                        -minId=0.35
                        -minCover=0.25
                  #elif $assembly_category == "well-ordered"
                        -minId=0.35
                        -minCover=0.15
                  #else
                        -minId=0.33
                        -minAlnSize=80
                  #end if
            #end if
            -minQSize=20 
            -ignoreIntrons 
            -repsAsMatch 
            -ignoreNs 
            -bestOverlap 
            -polyASizes=query.polyA 
            output.reps.psl 
            '${output_filtered}'
]]></command>
      <inputs>
            <param type="data" name="alignment" format="psl" />
            <param type="data" name="query" format="fasta" />
            <param name="assembly_type" type="select" label="Choose your type of cDNA sequence">
                  <option value="native">Same species</option>
                  <option value="xeno">Across species</option>
            </param>
            <param name="assembly_category" type="select" label="Choose your genome assembly category">
                  <option value="finished">finished assemblies (high quality)</option>
                  <option value="well-ordered">well-ordered assemblies (well ordered, whole genome shotgun)</option>
                  <option value="low-coverage">low-coverage assemblies (low coverage (&lt; 4x"), lots of contigs, N50 scaffold size &lt; 1mb) </option>
            </param>
      </inputs>
      <outputs>
            <data format="psl" name="output_filtered" label="${tool.name} on ${on_string}:filtered BLAT results"></data>
      </outputs>
  <tests>
      <test>
            <param name="alignment" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" />
            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
            <param name="assembly_type" value="xeno" />
            <param name="assembly_category" value="well-ordered" />
            <output name="output_filtered" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl" />
      </test>
      <test>
            <param name="alignment" value="dbia3/dbia3.sorted.psl" />
            <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
            <param name="assembly_type" value="xeno" />
            <param name="assembly_category" value="well-ordered" />
            <output name="output_filtered" value="dbia3/dbia3_dmel_filtered.psl" />
      </test>

  </tests> 
  <help>
        <![CDATA[

pslCDnaFilter (version: v340)
==============================
Filter cDNA alignments in psl format. Filtering criteria are comparative, selecting near best in genome alignments for each given cDNA and non-comparative, based only on the quality of an individual alignment.

usage:
-------

  $ pslCDnaFilter [options] inPsl outPsl

Source code:
-------------

http://hgdownload.cse.ucsc.edu/admin/exe/

Licence
========
Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).
]]>
</help>  
<citations>
      <citation type="bibtex">@article{kent2002blat,
  title={BLAT—the BLAST-like alignment tool},
  author={Kent, W James},
  journal={Genome research},
  volume={12},
  number={4},
  pages={656--664},
  year={2002},
  publisher={Cold Spring Harbor Lab}
      }</citation>
</citations> 
</tool>