comparison emboss_compseq.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
comparison
equal deleted inserted replaced
9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
2 <description>Count composition of dimer/trimer/etc words in a sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>On query</label>
8 </param>
9 <param name="word" type="text" value="2">
10 <label>Size of word (window) to count</label>
11 </param>
12 <param name="frame" type="select">
13 <label>Frame to inspect</label>
14 <option value="0">All Frames</option>
15 <option value="1">Frame 1</option>
16 <option value="2">Frame 2</option>
17 <option value="3">Frame 3</option>
18 </param>
19 </inputs>
20 <outputs>
21 <data format="compseq" name="out_file1" />
22 </outputs>
23 <tests>
24 <test>
25 <param name="input1" value="2.fasta"/>
26 <param name="word" value="2"/>
27 <param name="frame" value="0"/>
28 <output name="out_file1" file="emboss_compseq_out.compseq"/>
29 </test>
30 </tests>
31 <help>
32 .. class:: warningmark
33
34 The input dataset needs to be sequences.
35
36 -----
37
38 You can view the original documentation here_.
39
40 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
41
42 ------
43
44 **Citation**
45
46 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;`_
47
48 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;`_
49 </help>
50 </tool>