Mercurial > repos > devteam > emboss_5
comparison emboss_palindrome.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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1 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0"> | |
2 <description>Looks for inverted repeats in a nucleotide sequence</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> | |
5 <inputs> | |
6 <param format="fasta" name="input1" type="data"> | |
7 <label>Sequences</label> | |
8 </param> | |
9 <param name="minpallen" type="text" value="10"> | |
10 <label>Minimum length of palindrome</label> | |
11 </param> | |
12 <param name="maxpallen" type="text" value="100"> | |
13 <label>Maximum length of palindrome</label> | |
14 </param> | |
15 <param name="gaplimit" type="text" value="100"> | |
16 <label>Maximum gap between repeated regions</label> | |
17 </param> | |
18 <param name="nummismatches" type="text" value="0"> | |
19 <label>Number of mismatches allowed</label> | |
20 </param> | |
21 <param name="overlap" type="select"> | |
22 <label>Report overlapping matches</label> | |
23 <option value="yes">Yes</option> | |
24 <option value="no">No</option> | |
25 </param> | |
26 </inputs> | |
27 <outputs> | |
28 <data format="palindrome" name="out_file1" /> | |
29 </outputs> | |
30 <tests> | |
31 <test> | |
32 <param name="input1" value="2.fasta"/> | |
33 <param name="minpallen" value="10"/> | |
34 <param name="maxpallen" value="100"/> | |
35 <param name="gaplimit" value="100"/> | |
36 <param name="nummismatches" value="0"/> | |
37 <param name="overlap" value="yes"/> | |
38 <output name="out_file1" file="emboss_palindrome_out.palindrome"/> | |
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/palindrome.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> |