Mercurial > repos > devteam > emboss_5
comparison emboss_tranalign.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 832c20329690 |
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9:511429456d3c | 10:d49956b87f7e |
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1 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> | |
2 <description>Align nucleic coding regions given the aligned proteins</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto</command> | |
9 <inputs> | |
10 <param name="input1" type="data" format="fasta" label="Nucleic sequences" /> | |
11 <param name="input2" type="data" format="data" label="Protein sequences" /> | |
12 <param name="table" type="select" label="Code to use"> | |
13 <option value="0">Standard</option> | |
14 <option value="1">Standard (with alternative initiation codons)</option> | |
15 <option value="2">Vertebrate Mitochondrial</option> | |
16 <option value="3">Yeast Mitochondrial</option> | |
17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
18 <option value="5">Invertebrate Mitochondrial</option> | |
19 <option value="6">Ciliate Macronuclear and Dasycladacean</option> | |
20 <option value="9">Echinoderm Mitochondrial</option> | |
21 <option value="10">Euplotid Nuclear</option> | |
22 <option value="11">Bacterial</option> | |
23 <option value="12">Alternative Yeast Nuclear</option> | |
24 <option value="13">Ascidian Mitochondrial</option> | |
25 <option value="14">Flatworm Mitochondrial</option> | |
26 <option value="15">Blepharisma Macronuclear</option> | |
27 <option value="16">Chlorophycean Mitochondrial</option> | |
28 <option value="21">Trematode Mitochondrial</option> | |
29 <option value="22">Scenedesmus obliquus</option> | |
30 <option value="23">Thraustochytrium Mitochondrial</option> | |
31 </param> | |
32 <param name="out_format1" type="select" label="Output sequence file format"> | |
33 <option value="fasta">FASTA (m)</option> | |
34 <option value="acedb">ACeDB (m)</option> | |
35 <option value="asn1">ASN.1 (m)</option> | |
36 <option value="clustal">Clustal (m)</option> | |
37 <option value="codata">CODATA (m)</option> | |
38 <option value="embl">EMBL (m)</option> | |
39 <option value="fitch">Fitch (m)</option> | |
40 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> | |
41 <option value="genbank">GENBANK (m)</option> | |
42 <option value="gff">GFF (m)</option> | |
43 <option value="hennig86">Hennig86 (m)</option> | |
44 <option value="ig">Intelligenetics (m)</option> | |
45 <option value="jackknifer">Jackknifer (m)</option> | |
46 <option value="jackknifernon">Jackknifernon (m)</option> | |
47 <option value="mega">Mega (m)</option> | |
48 <option value="meganon">Meganon (m)</option> | |
49 <option value="msf">Wisconsin Package GCG's MSF (m)</option> | |
50 <option value="pir">NBRF (PIR) (m)</option> | |
51 <option value="ncbi">NCBI style FASTA (m)</option> | |
52 <option value="nexus">Nexus/PAUP (m)</option> | |
53 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> | |
54 <option value="phylip">PHYLIP interleaved (m)</option> | |
55 <option value="phylipnon">PHYLIP non-interleaved (m)</option> | |
56 <option value="selex">SELEX (m)</option> | |
57 <option value="staden">Staden (s)</option> | |
58 <option value="strider">DNA strider (m)</option> | |
59 <option value="swiss">SwisProt entry (m)</option> | |
60 <option value="text">Plain sequence (s)</option> | |
61 <option value="treecon">Treecon (m)</option> | |
62 </param> | |
63 </inputs> | |
64 <outputs> | |
65 <data name="out_file1" format="fasta" /> | |
66 </outputs> | |
67 <tests> | |
68 <test> | |
69 <param name="input1" value="3.fasta"/> | |
70 <param name="input2" value="2.pep"/> | |
71 <param name="table" value="0"/> | |
72 <param name="out_format1" value="fasta"/> | |
73 <output name="out_file1" file="emboss_tranalign_out.fasta"/> | |
74 </test> | |
75 </tests> | |
76 <help> | |
77 You can view the original documentation here_. | |
78 | |
79 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html | |
80 </help> | |
81 <expand macro="citations" /> | |
82 </tool> |