Mercurial > repos > devteam > emboss_5

comparison emboss_diffseq.xml @ 10:9b98d3d903c6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
2 <description>Find differences between nearly identical sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
5 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
6 <inputs>
7 <param format="data" name="input1" type="data">
8 <label>Sequence 1</label>
9 </param>
10 <param format="data" name="input2" type="data">
11 <label>Sequence 2</label>
12 </param>
13 <param name="wordsize" type="text" value="20">
14 <label>Wordsize</label>
15 </param>
16 <param name="globaldifferences" type="select">
17 <label>Report differences at the ends</label>
18 <option value="no">No</option>
19 <option value="yes">Yes</option>
20 </param>
21 <param name="out_format1" type="select">
22 <label>Output Report File Format</label>
23 <option value="diffseq">Diffseq</option>
24 <option value="embl">EMBL</option>
25 <option value="genbank">GENBANK</option>
26 <option value="gff">GFF</option>
27 <option value="pir">PIR</option>
28 <option value="swiss">SwissProt</option>
29 <option value="dbmotif">DbMotif</option>
30 <option value="excel">Excel (tab delimited)</option>
31 <option value="feattable">FeatTable</option>
32 <option value="motif">Motif</option>
33 <option value="regions">Regions</option>
34 <option value="seqtable">SeqTable</option>
35 <option value="simple">SRS Simple</option>
36 <option value="srs">SRS</option>
37 <option value="table">Table</option>
38 <option value="tagseq">TagSeq</option>
39 </param>
40 <param name="out_format2" type="select">
41 <label>Sequence 1 Output Feature File Format</label>
42 <option value="gff">GFF</option>
43 <option value="embl">EMBL</option>
44 <option value="swiss">SwissProt</option>
45 </param>
46 <param name="out_format3" type="select">
47 <label>Sequence 2 Output Feature File Format</label>
48 <option value="gff">GFF</option>
49 <option value="embl">EMBL</option>
50 <option value="swiss">SwissProt</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data format="diffseq" name="out_file1" />
55 <data format="gff" name="out_file2" />
56 <data format="gff" name="out_file3" />
57 </outputs>
58 <code file="emboss_format_corrector.py" />
59 <help>
60 You can view the original documentation here_.
61
62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
63
64 ------
65
66 **Citation**
67
68 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
69
70 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
71 </help>
72 </tool>