Mercurial > repos > devteam > emboss_5
comparison emboss_wobble.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author | devteam |
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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: wobble108" name="wobble" version="5.0.0"> | |
2 <description>Wobble base plot</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command> | |
5 <inputs> | |
6 <param format="fasta" name="input1" type="data"> | |
7 <label>Sequence</label> | |
8 </param> | |
9 <param name="window" type="text" value="30"> | |
10 <label>Window size, in codons</label> | |
11 </param> | |
12 <param name="bases" type="text" value="GC"> | |
13 <label>Bases used</label> | |
14 </param> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="png" name="ofile1" /> | |
18 <data format="wobble" name="ofile2" /> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="input1" value="2.fasta"/> | |
23 <param name="window" value="30"/> | |
24 <param name="bases" value="GC"/> | |
25 <output name="ofile2" file="emboss_wobble_out.wobble"/> | |
26 </test> | |
27 </tests> | |
28 <help> | |
29 | |
30 .. class:: warningmark | |
31 | |
32 The input dataset needs to be sequences. | |
33 | |
34 ----- | |
35 | |
36 You can view the original documentation here_. | |
37 | |
38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wobble.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> |