Mercurial > repos > devteam > emboss_5
comparison emboss_matcher.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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| 9:18a63c800a4d | 10:9b98d3d903c6 |
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| 1 <tool id="EMBOSS: matcher52" name="matcher" version="5.0.0"> | |
| 2 <description>Finds the best local alignments between two sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="data" name="input1" type="data"> | |
| 7 <label>Sequence 1</label> | |
| 8 </param> | |
| 9 <param format="data" name="input2" type="data"> | |
| 10 <label>Sequence 2</label> | |
| 11 </param> | |
| 12 <param name="alternatives" type="text" value="1"> | |
| 13 <label>Number of alternative matches</label> | |
| 14 </param> | |
| 15 <param name="gapopen" type="text" value="16"> | |
| 16 <label>Gap penalty</label> | |
| 17 </param> | |
| 18 <param name="gapextend" type="text" value="4"> | |
| 19 <label>Gap length (extension) penalty</label> | |
| 20 </param> | |
| 21 <param name="out_format1" type="select"> | |
| 22 <label>Output Alignment File Format</label> | |
| 23 <option value="markx0">Markx0 (p)</option> | |
| 24 <option value="simple">Simple (m)</option> | |
| 25 <option value="fasta">FASTA (m)</option> | |
| 26 <option value="msf">MSF (m)</option> | |
| 27 <option value="srs">SRS (m)</option> | |
| 28 <option value="pair">Pair (p)</option> | |
| 29 <option value="markx1">Markx1 (p)</option> | |
| 30 <option value="markx2">Markx2 (p)</option> | |
| 31 <option value="markx3">Markx3 (p)</option> | |
| 32 <option value="markx10">Markx10 (p)</option> | |
| 33 <option value="srspair">SRS pair (p)</option> | |
| 34 <option value="score">Score (p)</option> | |
| 35 </param> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <data format="markx0" name="out_file1" /> | |
| 39 </outputs> | |
| 40 <tests> | |
| 41 <test> | |
| 42 <param name="input1" value="2.fasta"/> | |
| 43 <param name="input2" value="1.fasta"/> | |
| 44 <param name="alternatives" value="1"/> | |
| 45 <param name="gapopen" value="16"/> | |
| 46 <param name="gapextend" value="4"/> | |
| 47 <param name="out_format1" value="fasta"/> | |
| 48 <output name="out_file1" file="emboss_matcher_out.fasta"/> | |
| 49 </test> | |
| 50 </tests> | |
| 51 <code file="emboss_format_corrector.py" /> | |
| 52 <help> | |
| 53 You can view the original documentation here_. | |
| 54 | |
| 55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html | |
| 56 | |
| 57 ------ | |
| 58 | |
| 59 **Citation** | |
| 60 | |
| 61 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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
| 62 | |
| 63 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>`_ | |
| 64 </help> | |
| 65 </tool> |