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

リビジョン 2, 3.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="EMBOSS: vectorstrip106" name="vectorstrip" version="5.0.0">
2  <description>Strips out DNA between a pair of vector sequences</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb
5  "$linkerb" -osformat4 $out_format1 -auto</command>
6  <inputs>
7    <param format="fasta" name="input1" type="data">
8      <label>Sequences</label>
9    </param>
10    <param format="data" name="input2" type="data">
11      <label>Vector file</label>
12    </param>
13    <param name="mismatch" size="4" type="text" value="10">
14      <label>Max allowed percent mismatch</label>
15    </param>
16    <param name="besthits" type="select">
17      <label>Show only the best hits (minimize mismatches)</label>
18      <option value="yes">Yes</option>
19      <option value="no">No</option>
20    </param>
21    <param name="linkera" size="50" type="text" value="">
22      <label>The 5' sequence</label>
23    </param>
24    <param name="linkerb" size="50" type="text" value="">
25      <label>The 3' sequence</label>
26    </param>
27    <param name="out_format1" type="select">
28      <label>Output Sequence File Format</label>
29      <option value="fasta">FASTA (m)</option>
30      <option value="acedb">ACeDB (m)</option>
31      <option value="asn1">ASN.1 (m)</option>
32      <option value="clustal">Clustal (m)</option>
33      <option value="codata">CODATA (m)</option>
34      <option value="embl">EMBL (m)</option>
35      <option value="fitch">Fitch (m)</option>
36      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
37      <option value="genbank">GENBANK (m)</option>
38      <option value="gff">GFF (m)</option>
39      <option value="hennig86">Hennig86 (m)</option>
40      <option value="ig">Intelligenetics (m)</option>
41      <option value="jackknifer">Jackknifer (m)</option>
42      <option value="jackknifernon">Jackknifernon (m)</option>
43      <option value="mega">Mega (m)</option>
44      <option value="meganon">Meganon (m)</option>
45      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
46      <option value="pir">NBRF (PIR) (m)</option>
47      <option value="ncbi">NCBI style FASTA (m)</option>
48      <option value="nexus">Nexus/PAUP (m)</option>
49      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
50      <option value="phylip">PHYLIP interleaved (m)</option>
51      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
52      <option value="selex">SELEX (m)</option>
53      <option value="staden">Staden (s)</option>
54      <option value="strider">DNA strider (m)</option>
55      <option value="swiss">SwisProt entry (m)</option>
56      <option value="text">Plain sequence (s)</option>
57      <option value="treecon">Treecon (m)</option>
58    </param>
59  </inputs>
60  <outputs>
61    <data format="fasta" name="ofile1" />
62    <data format="vectorstrip" name="ofile2" />
63  </outputs>
64  <!--  <tests>
65    <test>
66      <param name="input1" value="1.fasta"/>
67      <param name="input2" value="2.fasta"/>
68      <param name="mismatch" value="10"/>
69      <param name="besthits" value="yes"/>
70      <param name="linkera" value=""/>
71      <param name="linkerb" value=""/>
72      <param name="out_format1" value="fasta"/>
73      <output name="ofile1" file="emboss_vectorstrip_out.fasta"/>
74    </test>
75  </tests> -->
76  <code file="emboss_format_corrector.py" />
77  <help>
78    You can view the original documentation here_.
79   
80    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html
81  </help>
82</tool>
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