Mercurial > repos > devteam > emboss_5
comparison emboss_oddcomp.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: oddcomp64" name="oddcomp" version="5.0.0"> | |
| 2 <!-- output contains file location info, commented out functional tests --> | |
| 3 <description>Find protein sequence regions with a biased composition</description> | |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 5 <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>Sequences</label> | |
| 9 </param> | |
| 10 <param format="data" name="input2" type="data"> | |
| 11 <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label> | |
| 12 </param> | |
| 13 <param name="window" type="text" value="30"> | |
| 14 <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label> | |
| 15 </param> | |
| 16 <param name="ignorebz" type="select"> | |
| 17 <label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words | |
| 18 containing them, just noting them in the count of 'Other' words</label> | |
| 19 <option value="yes">Yes</option> | |
| 20 <option value="no">No</option> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="oddcomp" name="out_file1" /> | |
| 25 </outputs> | |
| 26 <!-- <tests> | |
| 27 <test> | |
| 28 <param name="input1" value="2.fasta"/> | |
| 29 <param name="input2" value="emboss_compseq_out.compseq"/> | |
| 30 <param name="window" value="30"/> | |
| 31 <param name="ignorebz" value="yes"/> | |
| 32 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/> | |
| 33 </test> | |
| 34 </tests> --> | |
| 35 <help> | |
| 36 You can view the original documentation here_. | |
| 37 | |
| 38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html | |
| 39 | |
| 40 ------ | |
| 41 | |
| 42 **Citation** | |
| 43 | |
| 44 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>`_ | |
| 45 | |
| 46 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>`_ | |
| 47 </help> | |
| 48 </tool> |