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comparison tools/emboss_5/emboss_cutseq.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0">
2 <description>Removes a specified section from a sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>On query</label>
8 </param>
9 <param name="from" size="8" type="text" value="1">
10 <label>Start of region to delete</label>
11 </param>
12 <param name="to" size="8" type="text" value="1">
13 <label>End of region to delete</label>
14 </param>
15 <param name="out_format1" type="select">
16 <label>Output Sequence File Format</label>
17 <option value="fasta">FASTA (m)</option>
18 <option value="acedb">ACeDB (m)</option>
19 <option value="asn1">ASN.1 (m)</option>
20 <option value="clustal">Clustal (m)</option>
21 <option value="codata">CODATA (m)</option>
22 <option value="embl">EMBL (m)</option>
23 <option value="fitch">Fitch (m)</option>
24 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
25 <option value="genbank">GENBANK (m)</option>
26 <option value="gff">GFF (m)</option>
27 <option value="hennig86">Hennig86 (m)</option>
28 <option value="ig">Intelligenetics (m)</option>
29 <option value="jackknifer">Jackknifer (m)</option>
30 <option value="jackknifernon">Jackknifernon (m)</option>
31 <option value="mega">Mega (m)</option>
32 <option value="meganon">Meganon (m)</option>
33 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
34 <option value="pir">NBRF (PIR) (m)</option>
35 <option value="ncbi">NCBI style FASTA (m)</option>
36 <option value="nexus">Nexus/PAUP (m)</option>
37 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
38 <option value="phylip">PHYLIP interleaved (m)</option>
39 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
40 <option value="selex">SELEX (m)</option>
41 <option value="staden">Staden (s)</option>
42 <option value="strider">DNA strider (m)</option>
43 <option value="swiss">SwisProt entry (m)</option>
44 <option value="text">Plain sequence (s)</option>
45 <option value="treecon">Treecon (m)</option>
46 </param>
47 </inputs>
48 <outputs>
49 <data format="fasta" name="out_file1" />
50 </outputs>
51 <tests>
52 <test>
53 <param name="input1" value="2.fasta"/>
54 <param name="from" value="1"/>
55 <param name="to" value="1"/>
56 <param name="out_format1" value="fasta"/>
57 <output name="out_file1" file="emboss_cutseq_out.fasta"/>
58 </test>
59 </tests>
60 <code file="emboss_format_corrector.py" />
61 <help>
62 .. class:: warningmark
63
64 The input dataset needs to be sequences.
65
66 -----
67
68 You can view the original documentation here_.
69
70 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cutseq.html
71 </help>
72 </tool>