<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1">
  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
  -invalid $invalid -map $map -graph png -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
    <param name="order" type="select" label="Sort by">
      <option value="3">Score</option>
      <option value="1">Length</option>
      <option value="2">Position</option>
    </param>
    <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
    <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data name="ofile2" format="png" />
    <data name="ofile1" format="epestfind" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="10"/>
      <param name="order" value="3"/>
      <param name="threshold" value="5.0"/>
      <param name="potential" value="yes"/>
      <param name="poor" value="yes"/>
      <param name="invalid" value="no"/>
      <param name="map" value="yes"/>
      <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
    </test>
  </tests>  output file contains file location info  -->
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html
  </help>
  <expand macro="citations" />
</tool>