annotate emboss_wordmatch.xml @ 13:8992d258e42f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: wordmatch110" name="wordmatch" version="@VERSION@.1">
  <description>Finds all exact matches of a given size between 2 sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2
  -offormat5 $out_format3 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence 1" />
    <param name="input2" type="data" format="fasta" label="Sequence 2" />
    <param name="wordsize" type="integer" value="4" label="Word size" />
    <param name="out_format1" type="select" label="Output alignment file format">
      <option value="match">Match (m)</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="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>
    <param name="out_format2" type="select" label="Output feature 1 file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
    <param name="out_format3" type="select" label="Output feature 2 file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="match" />
    <data name="out_file2" format="gff" />
    <data name="out_file3" format="gff" />
  </outputs>
  <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="wordsize" value="4"/>
      <param name="out_format1" value="fasta"/>
      <param name="out_format2" value="gff"/>
      <param name="out_format3" value="gff"/>
      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
    </test>
  </tests> test takes a long time to run-->
  <help>
.. class:: warningmark

The input datasets need to be sequences.

-----

    You can view the original documentation here_.

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