comparison emboss_prettyseq.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
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
2 <description>Output sequence with translated ranges</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>Sequence</label>
8 </param>
9 <param name="ruler" type="select">
10 <label>Add a ruler</label>
11 <option value="yes">Yes</option>
12 <option value="no">No</option>
13 </param>
14 <param name="plabel" type="select">
15 <label>Number translations</label>
16 <option value="yes">Yes</option>
17 <option value="no">No</option>
18 </param>
19 <param name="nlabel" type="select">
20 <label>Number DNA sequence</label>
21 <option value="yes">Yes</option>
22 <option value="no">No</option>
23 </param>
24 <param name="width" type="text" value="60">
25 <label>Width of screen</label>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="prettyseq" name="out_file1" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input1" value="2.fasta"/>
34 <param name="ruler" value="yes"/>
35 <param name="plabel" value="yes"/>
36 <param name="nlabel" value="yes"/>
37 <param name="width" value="60"/>
38 <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/>
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/prettyseq.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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
60 </help>
61 </tool>