Mercurial > repos > xuebing > sharplabtool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 <tool id="EMBOSS: merger54" name="merger" version="5.0.0">
2 <description>Merge two overlapping nucleic acid sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
5 <inputs>
6 <param format="data" name="input1" type="data">
7 <label>Sequence 1</label>
8 </param>
9 <param format="data" name="input2" type="data">
10 <label>Sequence 2</label>
11 </param>
12 <param name="gapopen" size="4" type="text" value="50.0">
13 <label>Gap opening penalty</label>
14 </param>
15 <param name="gapextend" size="4" type="text" value="5.0">
16 <label>Gap extension penalty</label>
17 </param>
18 <param name="out_format1" type="select">
19 <label>Output Sequence File Format</label>
20 <option value="fasta">FASTA (m)</option>
21 <option value="acedb">ACeDB (m)</option>
22 <option value="asn1">ASN.1 (m)</option>
23 <option value="clustal">Clustal (m)</option>
24 <option value="codata">CODATA (m)</option>
25 <option value="embl">EMBL (m)</option>
26 <option value="fitch">Fitch (m)</option>
27 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
28 <option value="genbank">GENBANK (m)</option>
29 <option value="gff">GFF (m)</option>
30 <option value="hennig86">Hennig86 (m)</option>
31 <option value="ig">Intelligenetics (m)</option>
32 <option value="jackknifer">Jackknifer (m)</option>
33 <option value="jackknifernon">Jackknifernon (m)</option>
34 <option value="mega">Mega (m)</option>
35 <option value="meganon">Meganon (m)</option>
36 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
37 <option value="pir">NBRF (PIR) (m)</option>
38 <option value="ncbi">NCBI style FASTA (m)</option>
39 <option value="nexus">Nexus/PAUP (m)</option>
40 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
41 <option value="phylip">PHYLIP interleaved (m)</option>
42 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
43 <option value="selex">SELEX (m)</option>
44 <option value="staden">Staden (s)</option>
45 <option value="strider">DNA strider (m)</option>
46 <option value="swiss">SwisProt entry (m)</option>
47 <option value="text">Plain sequence (s)</option>
48 <option value="treecon">Treecon (m)</option>
49 </param>
50 <param name="out_format2" type="select">
51 <label>Output Alignment File Format</label>
52 <option value="simple">Simple (m)</option>
53 <option value="fasta">FASTA (m)</option>
54 <option value="msf">MSF (m)</option>
55 <option value="srs">SRS (m)</option>
56 <option value="pair">Pair (p)</option>
57 <option value="markx0">Markx0 (p)</option>
58 <option value="markx1">Markx1 (p)</option>
59 <option value="markx2">Markx2 (p)</option>
60 <option value="markx3">Markx3 (p)</option>
61 <option value="markx10">Markx10 (p)</option>
62 <option value="srspair">SRS pair (p)</option>
63 <option value="score">Score (p)</option>
64 </param>
65 </inputs>
66 <outputs>
67 <data format="fasta" name="out_file1" />
68 <data format="simple" name="out_file2" />
69 </outputs>
70 <code file="emboss_format_corrector.py" />
71 <help>
72 You can view the original documentation here_.
73
74 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html
75 </help>
76 </tool>