annotate emboss_water.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

<tool id="EMBOSS: water107" name="water" version="5.0.0.1">
  <description>Smith-Waterman local alignment</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -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="gapopen" type="float" value="10.0" label="Gap open penalty" />
    <param name="gapextend" type="float" value="0.5" label="Gap extension penalty" />
    <param name="brief" type="select" label="Brief identity and similarity">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format1" type="select" label="Output alignment file format">
      <option value="srs">SRS (m)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (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="out_file1" format="srs" />
  </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="brief" value="no"/>
      <param name="out_format1" value="score"/>
      <output name="out_file1" file="emboss_water_out.score"/>
    </test>
  </tests>
  <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/water.html
  </help>
  <expand macro="citations" />
</tool>