view pslCheck.xml @ 1:97fd1b4df43a draft default tip

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<?xml version="1.0"?>
<tool id="ucsc_pslcheck" name="UCSC pslCheck" version="1.1">
    <description>validate PSL files</description>
    <requirements>
      <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="warning" description="invalid entries" />
    </stdio>
    <command><![CDATA[
        faSize -detailed -tab '${query}' > query_sizes
        && faSize -detailed -tab '${database}' > database_sizes 
        && pslCheck 
            -targetSizes=database_sizes
            -querySizes=query_sizes
            -pass='${pass_psl}'
            '${input_psl}'
]]></command>
      <inputs>
            <param type="data" name="database" format="fasta" />
            <param type="data" name="query" format="fasta" />
            <param type="data" name="input_psl" format="psl" />
      </inputs>
      <outputs>
            <data format="psl" name="pass_psl" label="${tool.name} on ${on_string}: valid"></data>
      </outputs>
  <tests>
      <test>
            <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
            <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
            <param name="input_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl" />
            <output name="pass_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl" />
      </test>
      <test>
            <param name="database" value="dbia3/dbia3.fa" />
            <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
            <param name="input_psl" value="dbia3/dbia3_dmel_filtered.psl" />
            <output name="pass_psl" value="dbia3/dbia3_dmel_filtered_valid.psl" />
      </test>

  </tests> 
  <help>
        <![CDATA[
pslCheck - validate PSL files
==============================

usage:

   $ pslCheck fileTbl(s)

options:
   
   -pass=pslFile - write PSLs without errors to this file

   -targetSizes=sizesFile - tab file with columns of target and size.

    If specified, psl is check to have a valid target and target
    coordinates.

   -querySizes=sizesFile - file with query sizes.

Source code (v340):
++++++++++++++++++++

userApps.v340.src.tgz: http://hgdownload.cse.ucsc.edu/admin/exe/

]]></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>