Mercurial > repos > devteam > emboss_5
comparison emboss_compseq.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: compseq14" name="compseq" version="5.0.0"> | |
| 2 <description>Count composition of dimer/trimer/etc words in a sequence</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>On query</label> | |
| 8 </param> | |
| 9 <param name="word" type="text" value="2"> | |
| 10 <label>Size of word (window) to count</label> | |
| 11 </param> | |
| 12 <param name="frame" type="select"> | |
| 13 <label>Frame to inspect</label> | |
| 14 <option value="0">All Frames</option> | |
| 15 <option value="1">Frame 1</option> | |
| 16 <option value="2">Frame 2</option> | |
| 17 <option value="3">Frame 3</option> | |
| 18 </param> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="compseq" name="out_file1" /> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="input1" value="2.fasta"/> | |
| 26 <param name="word" value="2"/> | |
| 27 <param name="frame" value="0"/> | |
| 28 <output name="out_file1" file="emboss_compseq_out.compseq"/> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 .. class:: warningmark | |
| 33 | |
| 34 The input dataset needs to be sequences. | |
| 35 | |
| 36 ----- | |
| 37 | |
| 38 You can view the original documentation here_. | |
| 39 | |
| 40 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html | |
| 41 | |
| 42 ------ | |
| 43 | |
| 44 **Citation** | |
| 45 | |
| 46 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>`_ | |
| 47 | |
| 48 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>`_ | |
| 49 </help> | |
| 50 </tool> |