comparison emboss_polydot.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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children 0e2484b6829b
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: polydot77" name="polydot" version="5.0.0">
2 <!-- produces png file, not added functional tests -->
3 <description>Displays all-against-all dotplots of a set of sequences</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
6 $gap -auto</command>
7 <inputs>
8 <param format="fasta" name="input1" type="data">
9 <label>Sequence</label>
10 </param>
11 <param name="wordsize" type="text" value="6">
12 <label>Word size</label>
13 </param>
14 <param name="boxit" type="select">
15 <label>Draw a box around each dotplot</label>
16 <option value="yes">Yes</option>
17 <option value="no">No</option>
18 </param>
19 <param name="gap" type="text" value="10">
20 <label>Size of gap</label>
21 </param>
22 </inputs>
23 <outputs>
24 <data format="polydot" name="output1" />
25 <data format="png" name="output2" />
26 </outputs>
27 <!-- <tests>
28 <test>
29 <param name="input1" value="2.fasta"/>
30 <param name="wordsize" value="6"/>
31 <param name="boxit" value="yes"/>
32 <param name="gap" value="10"/>
33 <output name="output1" file="emboss_polydot_out.png"/>
34 </test>
35 </tests>-->
36 <help>
37
38 .. class:: warningmark
39
40 The input dataset needs to be sequences.
41
42 -----
43
44 You can view the original documentation here_.
45
46 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html
47
48 ------
49
50 **Citation**
51
52 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;`_
53
54 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;`_
55 </help>
56 </tool>