view emboss_supermatcher.xml @ 19:d0847fe9b443 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"

<tool id="EMBOSS: supermatcher95" name="supermatcher" version="@VERSION@.1">
  <!-- puts file information in output report -->
  <description>Match large sequences against one or more other sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3
  $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Large sequences" />
    <param name="input2" type="data" format="data" label="Sequences to match" />
    <param name="gapopen" type="float" value="10.0" label="Gap opening penalty" />
    <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
    <param name="width" type="integer" value="16" label="Alignment width" />
    <param name="wordlen" type="integer" value="6" label="Word length for initial matching" />
    <param name="out_format1" type="select" label="Output alignment file format">
      <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="markx0">Markx0 (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="ofile1" format="simple" />
    <data name="ofile2" format="supermatcher" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="gapopen" value="10.0"/>
      <param name="gapextend" value="0.5"/>
      <param name="width" value="16"/>
      <param name="wordlen" value="6"/>
      <param name="out_format1" value="fasta"/>
      <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
    </test>
  </tests> -->
  <help>
    You can view the original documentation here_.

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