Mercurial > repos > devteam > emboss_5
comparison emboss_polydot.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: polydot77" name="polydot" version="5.0.0"> | |
| 2 <!-- produces png file, not added functional tests --> | |
| 3 <description>Displays all-against-all dotplots of a set of sequences</description> | |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap | |
| 6 $gap -auto</command> | |
| 7 <inputs> | |
| 8 <param format="fasta" name="input1" type="data"> | |
| 9 <label>Sequence</label> | |
| 10 </param> | |
| 11 <param name="wordsize" type="text" value="6"> | |
| 12 <label>Word size</label> | |
| 13 </param> | |
| 14 <param name="boxit" type="select"> | |
| 15 <label>Draw a box around each dotplot</label> | |
| 16 <option value="yes">Yes</option> | |
| 17 <option value="no">No</option> | |
| 18 </param> | |
| 19 <param name="gap" type="text" value="10"> | |
| 20 <label>Size of gap</label> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="polydot" name="output1" /> | |
| 25 <data format="png" name="output2" /> | |
| 26 </outputs> | |
| 27 <!-- <tests> | |
| 28 <test> | |
| 29 <param name="input1" value="2.fasta"/> | |
| 30 <param name="wordsize" value="6"/> | |
| 31 <param name="boxit" value="yes"/> | |
| 32 <param name="gap" value="10"/> | |
| 33 <output name="output1" file="emboss_polydot_out.png"/> | |
| 34 </test> | |
| 35 </tests>--> | |
| 36 <help> | |
| 37 | |
| 38 .. class:: warningmark | |
| 39 | |
| 40 The input dataset needs to be sequences. | |
| 41 | |
| 42 ----- | |
| 43 | |
| 44 You can view the original documentation here_. | |
| 45 | |
| 46 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html | |
| 47 | |
| 48 ------ | |
| 49 | |
| 50 **Citation** | |
| 51 | |
| 52 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>`_ | |
| 53 | |
| 54 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>`_ | |
| 55 </help> | |
| 56 </tool> |