Mercurial > repos > devteam > emboss_5
comparison emboss_cpgplot.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 |
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children | 0e2484b6829b |
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9:18a63c800a4d | 10:9b98d3d903c6 |
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1 <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0"> | |
2 <description>Plot CpG rich areas</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command> | |
5 <inputs> | |
6 <param format="data" name="input1" type="data"> | |
7 <label>On query</label> | |
8 </param> | |
9 <param name="window" type="integer" value="100"> | |
10 <label>Window Size</label> | |
11 </param> | |
12 <param name="minlen" type="integer" value="200"> | |
13 <label>Minimum length</label> | |
14 </param> | |
15 <param name="minoe" type="float" value="0.6"> | |
16 <label>Minimum average observed to expected ratio</label> | |
17 </param> | |
18 <param name="minpc" type="float" value="50.0"> | |
19 <label>Minimum average percentage of G plus C</label> | |
20 </param> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="cpgplot" name="outfile" /> | |
24 <data format="png" name="goutfile" /> | |
25 <data format="gff" name="outfeat" /> | |
26 </outputs> | |
27 <code file="emboss_format_corrector.py" /> | |
28 <help> | |
29 You can view the original documentation here_. | |
30 | |
31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html | |
32 | |
33 ------ | |
34 | |
35 **Citation** | |
36 | |
37 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>`_ | |
38 | |
39 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>`_ | |
40 </help> | |
41 </tool> |