annotate emboss_fuzznuc.xml @ 10:d49956b87f7e draft

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

<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2">
  <description>Nucleic acid pattern search</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="pattern" type="text" value="" label="Search pattern">
      <sanitizer>
        <valid initial="string.printable">
         <remove value="&apos;"/>
        </valid>
        <mapping initial="none">
          <add source="&apos;" target=""/>
        </mapping>
      </sanitizer>
    </param>
    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
    <param name="complement" type="select" label="Search complementary strand">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select" label="Output report file format">
      <option value="seqtable">SeqTable</option>
      <option value="embl">EMBL</option>
      <option value="genbank">GENBANK</option>
      <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="regions">Regions</option>
      <option value="simple">SRS Simple</option>
      <option value="fuzznuc">Fuzznuc Output File</option>
      <option value="srs">SRS</option>
      <option value="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fuzznuc" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="pattern" value="AA"/>
      <param name="mismatch" value="0"/>
      <param name="complement" value="no"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_fuzznuc_out.tabular"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

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