/tools/emboss_5/emboss_wordmatch.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 80 lines · 61 code · 8 blank · 11 comment · 0 complexity · 490e45a68d84f57b72b3b3f2cbbbc31a MD5 · raw file
- <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" size="5" 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="pair">Pair (p)</option>
- <option value="markx0">Markx0 (p)</option>
- <option value="markx1">Markx1 (p)</option>
- <option value="markx2">Markx2 (p)</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**
-
- 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>