|
0
|
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>
|
