root/galaxy-central/tools/emboss_5/emboss_shuffleseq.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: shuffleseq87" name="shuffleseq" version="5.0.0">
2  <!-- produces random outputs each time -->
3  <description>Shuffles a set of sequences maintaining composition</description>
4  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5  <command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command>
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>Sequences</label>
9    </param>
10    <param name="shuffle" size="4" type="text" value="1">
11      <label>Number of shuffles</label>
12    </param>
13    <param name="out_format1" type="select">
14      <label>Output Sequence File Format</label>
15      <option value="fasta">FASTA (m)</option>
16      <option value="acedb">ACeDB (m)</option>
17      <option value="asn1">ASN.1 (m)</option>
18      <option value="clustal">Clustal (m)</option>
19      <option value="codata">CODATA (m)</option>
20      <option value="embl">EMBL (m)</option>
21      <option value="fitch">Fitch (m)</option>
22      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
23      <option value="genbank">GENBANK (m)</option>
24      <option value="gff">GFF (m)</option>
25      <option value="hennig86">Hennig86 (m)</option>
26      <option value="ig">Intelligenetics (m)</option>
27      <option value="jackknifer">Jackknifer (m)</option>
28      <option value="jackknifernon">Jackknifernon (m)</option>
29      <option value="mega">Mega (m)</option>
30      <option value="meganon">Meganon (m)</option>
31      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
32      <option value="pir">NBRF (PIR) (m)</option>
33      <option value="ncbi">NCBI style FASTA (m)</option>
34      <option value="nexus">Nexus/PAUP (m)</option>
35      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
36      <option value="phylip">PHYLIP interleaved (m)</option>
37      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
38      <option value="selex">SELEX (m)</option>
39      <option value="staden">Staden (s)</option>
40      <option value="strider">DNA strider (m)</option>
41      <option value="swiss">SwisProt entry (m)</option>
42      <option value="text">Plain sequence (s)</option>
43      <option value="treecon">Treecon (m)</option>
44    </param>
45  </inputs>
46  <outputs>
47    <data format="fasta" name="out_file1" />
48  </outputs>
49  <code file="emboss_format_corrector.py" />
50  <help>
51
52.. class:: warningmark
53
54The input dataset needs to be sequences.
55
56-----
57
58    You can view the original documentation here_.
59   
60    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html
61  </help>
62</tool>
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