view emboss_marscan.xml @ 17:ce385837c160 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"

<tool id="EMBOSS: marscan49" name="marscan" version="@VERSION@">
  <description>Finds MAR/SAR sites in nucleic sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>marscan -sequence '$input1' -outfile '$out_file1' -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="out_format1" type="select" label="Output report file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="genbank">GENBANK</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="table">Table</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="gff" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_marscan_out.tabular"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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