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comparison tools/emboss_5/emboss_polydot.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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" size="10" 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" size="10" 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 </help>
48 </tool>