annotate emboss_helixturnhelix.xml @ 13:8992d258e42f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

<tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="@VERSION@.1">
  <description>Report nucleic acid binding motifs</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>helixturnhelix -sequence '$input1' -outfile '$out_file1' -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequences" />
    <param name="mean" type="float" value="238.71" label="Mean value" />
    <param name="sd" type="float" value="293.61" label="Standard deviation value" />
    <param name="minsd" type="float" value="2.5" label="Minimum SD" />
    <param name="eightyseven" type="select" label="Use the old (1987) weight data">
      <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="mean" value="238.71"/>
      <param name="sd" value="293.61"/>
      <param name="minsd" value="2.5"/>
      <param name="eightyseven" value="no"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_helixturnhelix_out.tabular"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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