view emboss_sigcleave.xml @ 20:21a9fb508031 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

<tool id="EMBOSS: sigcleave88" name="sigcleave" version="@VERSION@.1">
  <description>Reports protein signal cleavage sites</description>
  <expand macro="bio_tools" />
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>sigcleave -sequence '$input1' -outfile '$out_file1' -minweight $minweight -prokaryote $prokaryote -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequences" />
    <param name="minweight" type="float" value="3.5" label="Minimum scoring weight value for the predicted cleavage site" />
    <param name="prokaryote" type="select" label="Specifies the sequence is prokaryotic and changes the default scoring data file">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="out_format1" type="select" label="Output report file format">
      <option value="motif">Motif</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="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="motif" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minweight" value="3.5"/>
      <param name="prokaryote" value="no"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_sigcleave_out.tabular"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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