Mercurial > repos > devteam > emboss_5

comparison emboss_merger.xml @ 10:d49956b87f7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
parents
children 8992d258e42f
comparison
equal deleted inserted replaced
9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: merger54" name="merger" version="5.0.0.1">
2 <description>Merge two overlapping nucleic acid sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="data" label="Sequence 1" />
11 <param name="input2" type="data" format="data" label="Sequence 2" />
12 <param name="gapopen" type="float" value="50.0" label="Gap opening penalty" />
13 <param name="gapextend" type="float" value="5.0" label="Gap extension penalty" />
14 <param name="out_format1" type="select" label="Output sequence file format">
15 <option value="fasta">FASTA (m)</option>
16 <option value="acedb">ACeDB (m)</option>
17 <option value="asn1">ASN.1 (m)</option>
18 <option value="clustal">Clustal (m)</option>
19 <option value="codata">CODATA (m)</option>
20 <option value="embl">EMBL (m)</option>
21 <option value="fitch">Fitch (m)</option>
22 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
23 <option value="genbank">GENBANK (m)</option>
24 <option value="gff">GFF (m)</option>
25 <option value="hennig86">Hennig86 (m)</option>
26 <option value="ig">Intelligenetics (m)</option>
27 <option value="jackknifer">Jackknifer (m)</option>
28 <option value="jackknifernon">Jackknifernon (m)</option>
29 <option value="mega">Mega (m)</option>
30 <option value="meganon">Meganon (m)</option>
31 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
32 <option value="pir">NBRF (PIR) (m)</option>
33 <option value="ncbi">NCBI style FASTA (m)</option>
34 <option value="nexus">Nexus/PAUP (m)</option>
35 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
36 <option value="phylip">PHYLIP interleaved (m)</option>
37 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
38 <option value="selex">SELEX (m)</option>
39 <option value="staden">Staden (s)</option>
40 <option value="strider">DNA strider (m)</option>
41 <option value="swiss">SwisProt entry (m)</option>
42 <option value="text">Plain sequence (s)</option>
43 <option value="treecon">Treecon (m)</option>
44 </param>
45 <param name="out_format2" type="select" label="Output alignment file format">
46 <option value="simple">Simple (m)</option>
47 <option value="fasta">FASTA (m)</option>
48 <option value="msf">MSF (m)</option>
49 <option value="srs">SRS (m)</option>
50 <option value="pair">Pair (p)</option>
51 <option value="markx0">Markx0 (p)</option>
52 <option value="markx1">Markx1 (p)</option>
53 <option value="markx2">Markx2 (p)</option>
54 <option value="markx3">Markx3 (p)</option>
55 <option value="markx10">Markx10 (p)</option>
56 <option value="srspair">SRS pair (p)</option>
57 <option value="score">Score (p)</option>
58 </param>
59 </inputs>
60 <outputs>
61 <data name="out_file1" format="fasta" />
62 <data name="out_file2" format="simple" />
63 </outputs>
64 <help>
65 You can view the original documentation here_.
66
67 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/merger.html
68 </help>
69 <expand macro="citations" />
70 </tool>