comparison emboss_wordmatch.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: wordmatch110" name="wordmatch" version="5.0.0">
  <description>Finds all exact matches of a given size between 2 sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
  -offormat5 $out_format3 -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequence 1</label>
    </param>
    <param format="fasta" name="input2" type="data">
      <label>Sequence 2</label>
    </param>
    <param name="wordsize" type="text" value="4">
      <label>Word size</label>
    </param>
    <param name="out_format1" type="select">
      <label>Output Alignment File Format</label>
      <option value="match">Match (m)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>

      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
    <param name="out_format2" type="select">
      <label>Output Feature 1 File Format</label>
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
    <param name="out_format3" type="select">
      <label>Output Feature 2 File Format</label>
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data format="match" name="out_file1" />
    <data format="gff" name="out_file2" />
    <data format="gff" name="out_file3" />
  </outputs>
  <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="wordsize" value="4"/>
      <param name="out_format1" value="fasta"/>
      <param name="out_format2" value="gff"/>
      <param name="out_format3" value="gff"/>
      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
    </test> 
  </tests> test takes a long time to run-->
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark 

The input datasets need to be sequences. 

----- 

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.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: wordmatch110" name="wordmatch" version="5.0.0.1">
  <description>Finds all exact matches of a given size between 2 sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2
  -offormat5 $out_format3 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence 1" />
    <param name="input2" type="data" format="fasta" label="Sequence 2" />
    <param name="wordsize" type="integer" value="4" label="Word size" />
    <param name="out_format1" type="select" label="Output alignment file format">
      <option value="match">Match (m)</option>
      <option value="simple">Simple (m)</option>
      <option value="fasta">FASTA (m)</option>
      <option value="msf">MSF (m)</option>
      <option value="srs">SRS (m)</option>

      <option value="markx3">Markx3 (p)</option>
      <option value="markx10">Markx10 (p)</option>
      <option value="srspair">SRS pair (p)</option>
      <option value="score">Score (p)</option>
    </param>
    <param name="out_format2" type="select" label="Output feature 1 file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
    <param name="out_format3" type="select" label="Output feature 2 file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="match" />
    <data name="out_file2" format="gff" />
    <data name="out_file3" format="gff" />
  </outputs>
  <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="wordsize" value="4"/>
      <param name="out_format1" value="fasta"/>
      <param name="out_format2" value="gff"/>
      <param name="out_format3" value="gff"/>
      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
    </test>
  </tests> test takes a long time to run-->
  <help>
.. class:: warningmark

The input datasets need to be sequences.

-----

    You can view the original documentation here_.

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