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

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
2  <!-- puts file information in output report -->
3  <description>Match large sequences against one or more other sequences</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
6  $out_format1 -auto</command>
7  <inputs>
8    <param format="fasta" name="input1" type="data">
9      <label>Large sequences</label>
10    </param>
11    <param format="data" name="input2" type="data">
12      <label>Sequences to match</label>
13    </param>
14    <param name="gapopen" size="4" type="text" value="10.0">
15      <label>Gap opening penalty</label>
16    </param>
17    <param name="gapextend" size="4" type="text" value="0.5">
18      <label>Gap extension penalty</label>
19    </param>
20    <param name="width" size="4" type="text" value="16">
21      <label>Alignment width</label>
22    </param>
23    <param name="wordlen" size="4" type="text" value="6">
24      <label>Word length for initial matching</label>
25    </param>
26    <param name="out_format1" type="select">
27      <label>Output Alignment File Format</label>
28      <option value="simple">Simple (m)</option>
29      <option value="fasta">FASTA (m)</option>
30      <option value="msf">MSF (m)</option>
31      <option value="srs">SRS (m)</option>
32      <option value="pair">Pair (p)</option>
33      <option value="markx0">Markx0 (p)</option>
34      <option value="markx1">Markx1 (p)</option>
35      <option value="markx2">Markx2 (p)</option>
36      <option value="markx3">Markx3 (p)</option>
37      <option value="markx10">Markx10 (p)</option>
38      <option value="srspair">SRS pair (p)</option>
39      <option value="score">Score (p)</option>
40    </param>
41  </inputs>
42  <outputs>
43    <data format="simple" name="ofile1" />
44    <data format="supermatcher" name="ofile2" />
45  </outputs>
46<!--    <tests>
47    <test>
48      <param name="input1" value="2.fasta"/>
49      <param name="input2" value="1.fasta"/>
50      <param name="gapopen" value="10.0"/>
51      <param name="gapextend" value="0.5"/>
52      <param name="width" value="16"/>
53      <param name="wordlen" value="6"/>
54      <param name="out_format1" value="fasta"/>
55      <output name="ofile1" file="emboss_supermatcher_out.fasta"/>
56    </test>
57  </tests> -->
58  <code file="emboss_format_corrector.py" />
59  <help>
60    You can view the original documentation here_.
61   
62    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html
63  </help>
64</tool>
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