Mercurial > repos > devteam > emboss_5

comparison emboss_compseq.xml @ 11:0e2484b6829b 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-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0"> 1 <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0.1">
2 <description>Count composition of dimer/trimer/etc words in a sequence</description> 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> 3 <macros>
4 <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>compseq -sequence '$input1' -outfile '$out_file1' -word $word -frame $frame -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="On query" />
7 <label>On query</label> 10 <param name="word" type="integer" value="2" label="Size of word (window) to count" />
8 </param> 11 <param name="frame" type="select" label="Frame to inspect">
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> 12 <option value="0">All Frames</option>
15 <option value="1">Frame 1</option> 13 <option value="1">Frame 1</option>
16 <option value="2">Frame 2</option> 14 <option value="2">Frame 2</option>
17 <option value="3">Frame 3</option> 15 <option value="3">Frame 3</option>
18 </param> 16 </param>
19 </inputs> 17 </inputs>
20 <outputs> 18 <outputs>
21 <data format="compseq" name="out_file1" /> 19 <data name="out_file1" format="compseq" />
22 </outputs> 20 </outputs>
23 <tests> 21 <tests>
24 <test> 22 <test>
25 <param name="input1" value="2.fasta"/> 23 <param name="input1" value="2.fasta"/>
26 <param name="word" value="2"/> 24 <param name="word" value="2"/>
34 The input dataset needs to be sequences. 32 The input dataset needs to be sequences.
35 33
36 ----- 34 -----
37 35
38 You can view the original documentation here_. 36 You can view the original documentation here_.
39
40 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
41 37
42 ------ 38 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/compseq.html
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> 39 </help>
40 <expand macro="citations" />
50 </tool> 41 </tool>