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

リビジョン 2, 2.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0">
2  <description>All-against-all comparison of a set of sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="wordsize" size="4" type="text" value="4">
10      <label>Word size</label>
11    </param>
12    <param name="out_format1" type="select">
13      <label>Output Alignment File Format</label>
14      <option value="match">Match (m)</option>
15      <option value="simple">Simple (m)</option>
16      <option value="fasta">FASTA (m)</option>
17      <option value="msf">MSF (m)</option>
18      <option value="srs">SRS (m)</option>
19      <option value="pair">Pair (p)</option>
20      <option value="markx0">Markx0 (p)</option>
21      <option value="markx1">Markx1 (p)</option>
22      <option value="markx2">Markx2 (p)</option>
23      <option value="markx3">Markx3 (p)</option>
24      <option value="markx10">Markx10 (p)</option>
25      <option value="srspair">SRS pair (p)</option>
26      <option value="score">Score (p)</option>
27      <option value="seqmatchall">Seqmatchall Output File</option>
28    </param>
29  </inputs>
30  <outputs>
31    <data format="seqmatchall" name="out_file1" />.
32  </outputs>
33  <tests>
34    <test>
35      <param name="input1" value="2.fasta"/>
36      <param name="wordsize" value="2"/>
37      <param name="out_format1" value="fasta"/>
38      <output name="out_file1" file="emboss_seqmatchall_out.fasta"/>
39    </test>
40  </tests>
41  <code file="emboss_format_corrector.py" />
42  <help>
43
44.. class:: warningmark
45
46The input dataset needs to be sequences.
47
48-----
49
50    You can view the original documentation here_.
51   
52    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html
53  </help>
54</tool>
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