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comparison emboss_polydot.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: polydot77" name="polydot" version="5.0.0.1">
2 <!-- produces png file, not added functional tests -->
3 <description>Displays all-against-all dotplots of a set of sequences</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
9 $gap -auto</command>
10 <inputs>
11 <param name="input1" type="data" format="fasta" label="Sequence" />
12 <param name="wordsize" type="integer" value="6" label="Word size" />
13 <param name="boxit" type="select" label="Draw a box around each dotplot">
14 <option value="yes">Yes</option>
15 <option value="no">No</option>
16 </param>
17 <param name="gap" type="integer" value="10" label="Size of gap" />
18 </inputs>
19 <outputs>
20 <data name="output1" format="polydot" />
21 <data name="output2" format="png" />
22 </outputs>
23 <!-- <tests>
24 <test>
25 <param name="input1" value="2.fasta"/>
26 <param name="wordsize" value="6"/>
27 <param name="boxit" value="yes"/>
28 <param name="gap" value="10"/>
29 <output name="output1" file="emboss_polydot_out.png"/>
30 </test>
31 </tests>-->
32 <help>
33 .. class:: warningmark
34
35 The input dataset needs to be sequences.
36
37 -----
38
39 You can view the original documentation here_.
40
41 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/polydot.html
42 </help>
43 <expand macro="citations" />
44 </tool>