Mercurial > repos > devteam > emboss_5
comparison emboss_dotpath.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: dotpath25" name="dotpath" version="5.0.0"> | |
| 2 <description>Non-overlapping wordmatch dotplot of two sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png | |
| 5 -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>Sequence 1</label> | |
| 9 </param> | |
| 10 <param format="data" name="input2" type="data"> | |
| 11 <label>Sequence 2</label> | |
| 12 </param> | |
| 13 <param name="wordsize" type="text" value="4"> | |
| 14 <label>Word size (Integer 2 or more)</label> | |
| 15 </param> | |
| 16 <param name="overlaps" type="select"> | |
| 17 <label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label> | |
| 18 <option value="no">No</option> | |
| 19 <option value="yes">Yes</option> | |
| 20 </param> | |
| 21 <param name="boxit" type="select"> | |
| 22 <label>Draw a box around dotplot</label> | |
| 23 <option value="yes">Yes</option> | |
| 24 <option value="no">No</option> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="png" name="out_file1" /> | |
| 29 </outputs> | |
| 30 <!-- functional tests not possible since image output contains file name information and timestamp --> | |
| 31 <help> | |
| 32 You can view the original documentation here_. | |
| 33 | |
| 34 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html | |
| 35 | |
| 36 ------ | |
| 37 | |
| 38 **Citation** | |
| 39 | |
| 40 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>`_ | |
| 41 | |
| 42 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>`_ | |
| 43 </help> | |
| 44 </tool> |