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

リビジョン 2, 3.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

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1<tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
2  <description>Extract regions from a sequence</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="data" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="regions" size="20" type="text" value="1-9999999">
10      <label>Regions to extract</label>
11    </param>
12    <param name="separate" type="select">
13      <label>Write each specified region as a separate sequence</label>
14      <option value="no">No</option>
15      <option value="yes">Yes</option>
16    </param>
17    <param name="out_format1" type="select">
18      <label>Output Sequence File Format</label>
19      <option value="fasta">FASTA (m)</option>
20      <option value="acedb">ACeDB (m)</option>
21      <option value="asn1">ASN.1 (m)</option>
22      <option value="clustal">Clustal (m)</option>
23      <option value="codata">CODATA (m)</option>
24      <option value="embl">EMBL (m)</option>
25      <option value="fitch">Fitch (m)</option>
26      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
27      <option value="genbank">GENBANK (m)</option>
28      <option value="gff">GFF (m)</option>
29      <option value="hennig86">Hennig86 (m)</option>
30      <option value="ig">Intelligenetics (m)</option>
31      <option value="jackknifer">Jackknifer (m)</option>
32      <option value="jackknifernon">Jackknifernon (m)</option>
33      <option value="mega">Mega (m)</option>
34      <option value="meganon">Meganon (m)</option>
35      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
36      <option value="pir">NBRF (PIR) (m)</option>
37      <option value="ncbi">NCBI style FASTA (m)</option>
38      <option value="nexus">Nexus/PAUP (m)</option>
39      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
40      <option value="phylip">PHYLIP interleaved (m)</option>
41      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
42      <option value="selex">SELEX (m)</option>
43      <option value="staden">Staden (s)</option>
44      <option value="strider">DNA strider (m)</option>
45      <option value="swiss">SwisProt entry (m)</option>
46      <option value="text">Plain sequence (s)</option>
47      <option value="treecon">Treecon (m)</option>
48    </param>
49  </inputs>
50  <outputs>
51    <data format="fasta" name="out_file1" />
52  </outputs>
53  <tests>
54    <test>
55      <param name="input1" value="2.fasta"/>
56      <param name="regions" value="1-9999999"/>
57      <param name="separate" value="no"/>
58      <param name="out_format1" value="fasta"/>
59      <output name="out_file1" file="emboss_extractseq_out.fasta"/>
60    </test>
61  </tests>
62  <code file="emboss_format_corrector.py" />
63  <help>
64    You can view the original documentation here_.
65   
66    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html
67  </help>
68</tool>
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