annotate emboss_antigenic.xml @ 12:832c20329690 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115

<tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0.1">
  <description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>antigenic -sequence '$input1' -outfile '$out_file1' -minlen $minlen -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="On query" />
    <param name="minlen" type="integer" value="6" label="Minimum length of region" />
    <param name="out_format1" type="select" label="Output format">
      <option value="gff">GFF</option>
      <option value="pir">PIR</option>
      <option value="swiss">SwissProt</option>
      <option value="dbmotif">DbMotif</option>
      <option value="diffseq">diffseq</option>
      <option value="excel">Excel (TAB Delimited)</option>
      <option value="feattable">FeatTable</option>
      <option value="motif">Motif</option>
      <option value="nametable">NameTable</option>
      <option value="regions">Regions</option>
      <option value="seqtable">SeqTable</option>
      <option value="simple">SRS simple</option>
      <option value="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">Tagseq</option>
      <option value="antigenic">Antigenic Output File</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="antigenic" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minlen" value="6"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_antigenic_out.tabular"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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