annotate emboss_fuzztran.xml @ 14:2e0fb4bc860e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit fed02ef07e0a45f0d5a89cdca364607ab8da6cf9

<tool id="EMBOSS: fuzztran39" name="fuzztran" version="@VERSION@.1">
  <description>Protein pattern search after translation</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="pattern" type="text" value="" label="Search pattern" />
    <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
    <param name="frame" type="select" label="Frame(s) to translate">
      <option value="1">Frame 1</option>
      <option value="2">Frame 2</option>
      <option value="3">Frame 3</option>
      <option value="F">Forward three frames</option>
      <option value="-1">Frame -1</option>
      <option value="-2">Frame -2</option>
      <option value="-3">Frame -3</option>
      <option value="R">Reverse three frames</option>
      <option value="6">All six frames</option>
    </param>
    <param name="table" type="select" label="Code to use">
      <option value="0">Standard</option>
      <option value="1">Standard (with alternative initiation codons)</option>
      <option value="2">Vertebrate Mitochondrial</option>
      <option value="3">Yeast Mitochondrial</option>
      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
      <option value="5">Invertebrate Mitochondrial</option>
      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
      <option value="9">Echinoderm Mitochondrial</option>
      <option value="10">Euplotid Nuclear</option>
      <option value="11">Bacterial</option>
      <option value="12">Alternative Yeast Nuclear</option>
      <option value="13">Ascidian Mitochondrial</option>
      <option value="14">Flatworm Mitochondrial</option>
      <option value="15">Blepharisma Macronuclear</option>
      <option value="16">Chlorophycean Mitochondrial</option>
      <option value="21">Trematode Mitochondrial</option>
      <option value="22">Scenedesmus obliquus</option>
      <option value="23">Thraustochytrium Mitochondrial</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="fuzztran" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="pattern" value="AA"/>
      <param name="mismatch" value="0"/>
      <param name="frame" value="6"/>
      <param name="table" value="0"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_fuzztran_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/fuzztran.html
  </help>
  <expand macro="citations" />
</tool>