view emboss_etandem.xml @ 12:ace31bbde4c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9d484642914b581ce35f254466b849d3c4c2c06c

<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0.1">
  <description>Looks for tandem repeats in a nucleotide sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence" />
    <param name="minrepeat" type="integer" value="10" label="Minimum repeat size" />
    <param name="maxrepeat" type="integer" value="10" label="Maximum repeat size" />
    <param name="threshold" type="integer" value="20" label="Threshold score" />
    <param name="mismatch" type="select" label="Allow N as a mismatch">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="uniform" type="select" label="Allow uniform consensus">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select" label="Output report file format">
      <option value="table">Table</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="seqtable">SeqTable</option>
      <option value="simple">SRS Simple</option>
      <option value="srs">SRS</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="etandem" />
    <data name="ofile2" format="table" />
  </outputs>
    <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="minrepeat" value="10"/>
      <param name="maxrepeat" value="10"/>
      <param name="threshold" value="20"/>
      <param name="mismatch" value="no"/>
       <param name="uniform" value="no"/>
      <param name="out_format1" value="table"/>
      <output name="ofile2" file="emboss_etandem_out.table"/>
    </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/etandem.html
  </help>
  <expand macro="citations" />
</tool>