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comparison emboss_tranalign.xml @ 10:d49956b87f7e draft

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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
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children 832c20329690
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9:511429456d3c 10:d49956b87f7e
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>