view emboss_matcher.xml @ 17:bde3097ac0f6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit d5dfff2cd58b094e0e4a6f8dc475de5facd9700b"

<tool id="EMBOSS: matcher52" name="matcher" version="@VERSION@.1">
  <description>Finds the best local alignments between two sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>matcher -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence 1" />
    <param name="input2" type="data" format="data" label="Sequence 2" />
    <param name="alternatives" type="integer" value="1" label="Number of alternative matches" />
    <param name="gapopen" type="integer" value="16" label="Gap penalty" />
    <param name="gapextend" type="integer" value="4" label="Gap length (extension) penalty" />
    <param name="out_format1" type="select" label="Output alignment file format">
      <option value="markx0">Markx0 (p)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>
      <option value="pair">Pair (p)</option>
      <option value="markx1">Markx1 (p)</option>
      <option value="markx2">Markx2 (p)</option>
      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="markx0" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="alternatives" value="1"/>
      <param name="gapopen" value="16"/>
      <param name="gapextend" value="4"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_matcher_out.fasta"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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