root/galaxy-central/tools/emboss_5/emboss_polydot.xml

リビジョン 2, 1.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
40The 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>
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