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<?xml version="1.0"?>
<tool id="ucsc_pslpostarget" name="UCSC pslPosTarget" version="1.1">
    <description>flip psl strands so target is positive and implicit</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[
        pslPosTarget 
            '${input_psl}'
            '${output_psl}'
]]></command>
      <inputs>
            <param type="data" name="input_psl" format="psl" />
      </inputs>
      <outputs>
            <data format="psl" name="output_psl" label="${tool.name} on ${on_string}"></data>
      </outputs>
  <tests>
      <test>
            <param name="input_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl" />
            <output name="output_psl" value="amaVit1_Gallus/amaVit1_Gallus.pos.psl" />
      </test>
      <test>
            <param name="input_psl" value="dbia3/dbia3_dmel_filtered_valid.psl" />
            <output name="output_psl" value="dbia3/dbia3_dmel.pos.psl" />
      </test>

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

- flip psl strands so target is positive and implicit

usage:

   pslPosTarget inPsl outPsl

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>