Mercurial > repos > devteam > emboss_5
comparison emboss_prettyseq.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: prettyseq80" name="prettyseq" version="5.0.0"> | |
| 2 <description>Output sequence with translated ranges</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>Sequence</label> | |
| 8 </param> | |
| 9 <param name="ruler" type="select"> | |
| 10 <label>Add a ruler</label> | |
| 11 <option value="yes">Yes</option> | |
| 12 <option value="no">No</option> | |
| 13 </param> | |
| 14 <param name="plabel" type="select"> | |
| 15 <label>Number translations</label> | |
| 16 <option value="yes">Yes</option> | |
| 17 <option value="no">No</option> | |
| 18 </param> | |
| 19 <param name="nlabel" type="select"> | |
| 20 <label>Number DNA sequence</label> | |
| 21 <option value="yes">Yes</option> | |
| 22 <option value="no">No</option> | |
| 23 </param> | |
| 24 <param name="width" type="text" value="60"> | |
| 25 <label>Width of screen</label> | |
| 26 </param> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="prettyseq" name="out_file1" /> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="input1" value="2.fasta"/> | |
| 34 <param name="ruler" value="yes"/> | |
| 35 <param name="plabel" value="yes"/> | |
| 36 <param name="nlabel" value="yes"/> | |
| 37 <param name="width" value="60"/> | |
| 38 <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help> | |
| 42 | |
| 43 .. class:: warningmark | |
| 44 | |
| 45 The input dataset needs to be sequences. | |
| 46 | |
| 47 ----- | |
| 48 | |
| 49 You can view the original documentation here_. | |
| 50 | |
| 51 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html | |
| 52 | |
| 53 ------ | |
| 54 | |
| 55 **Citation** | |
| 56 | |
| 57 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>`_ | |
| 58 | |
| 59 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>`_ | |
| 60 </help> | |
| 61 </tool> |