comparison emboss_fuzztran.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
  <description>Protein pattern search after translation</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="pattern" type="text" value="">
      <label>Search pattern</label>
    </param>
    <param name="mismatch" type="text" value="0">
      <label>Number of mismatches</label>
    </param>
    <param name="frame" type="select">
      <label>Frame(s) to translate</label>
      <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</label>
      <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="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</label>
      <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="srs">SRS</option>
      <option value="tagseq">TagSeq</option>
    </param>
  </inputs>
  <outputs>
    <data format="fuzztran" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="pattern" value="AA"/>

      <param name="table" value="0"/>
      <param name="out_format1" value="excel"/>
      <output name="out_file1" file="emboss_fuzztran_out.tabular"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0.1">
  <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="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="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="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>