0
|
1 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
|
|
2 <description>Translate nucleic acid sequences</description>
|
|
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
4 <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
|
|
5 <inputs>
|
|
6 <param format="fasta" name="input1" type="data">
|
|
7 <label>Sequences</label>
|
|
8 </param>
|
|
9 <param name="frame" type="select">
|
|
10 <label>Frame(s) to translate</label>
|
|
11 <option value="1">Frame 1</option>
|
|
12 <option value="2">Frame 2</option>
|
|
13 <option value="3">Frame 3</option>
|
|
14 <option value="F">Forward three frames</option>
|
|
15 <option value="-1">Frame -1</option>
|
|
16 <option value="-2">Frame -2</option>
|
|
17 <option value="-3">Frame -3</option>
|
|
18 <option value="R">Reverse three frames</option>
|
|
19 <option value="6">All six frames</option>
|
|
20 </param>
|
|
21 <param name="table" type="select">
|
|
22 <label>Code to use</label>
|
|
23 <option value="0">Standard</option>
|
|
24 <option value="1">Standard (with alternative initiation codons)</option>
|
|
25 <option value="2">Vertebrate Mitochondrial</option>
|
|
26 <option value="3">Yeast Mitochondrial</option>
|
|
27 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
|
|
28 <option value="5">Invertebrate Mitochondrial</option>
|
|
29 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
|
|
30 <option value="9">Echinoderm Mitochondrial</option>
|
|
31 <option value="10">Euplotid Nuclear</option>
|
|
32 <option value="11">Bacterial</option>
|
|
33 <option value="12">Alternative Yeast Nuclear</option>
|
|
34 <option value="13">Ascidian Mitochondrial</option>
|
|
35 <option value="14">Flatworm Mitochondrial</option>
|
|
36 <option value="15">Blepharisma Macronuclear</option>
|
|
37 <option value="16">Chlorophycean Mitochondrial</option>
|
|
38 <option value="21">Trematode Mitochondrial</option>
|
|
39 <option value="22">Scenedesmus obliquus</option>
|
|
40 <option value="23">Thraustochytrium Mitochondrial</option>
|
|
41 </param>
|
|
42 <param name="regions" size="10" type="text" value="">
|
|
43 <label>Regions to translate</label>
|
|
44 </param>
|
|
45 <param name="trim" type="select">
|
|
46 <label>Remove all 'X' and '*' characters from the right end of the translation</label>
|
|
47 <option value="no">No</option>
|
|
48 <option value="yes">Yes</option>
|
|
49 </param>
|
|
50 <param name="clean" type="select">
|
|
51 <label>Change all STOP codon positions from the '*' character to 'X'</label>
|
|
52 <option value="no">No</option>
|
|
53 <option value="yes">Yes</option>
|
|
54 </param>
|
|
55 <param name="alternative" type="select">
|
|
56 <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
|
|
57 <option value="no">No</option>
|
|
58 <option value="yes">Yes</option>
|
|
59 </param>
|
|
60 <param name="out_format1" type="select">
|
|
61 <label>Output Sequence File Format</label>
|
|
62 <option value="fasta">FASTA (m)</option>
|
|
63 <option value="acedb">ACeDB (m)</option>
|
|
64 <option value="asn1">ASN.1 (m)</option>
|
|
65 <option value="clustal">Clustal (m)</option>
|
|
66 <option value="codata">CODATA (m)</option>
|
|
67 <option value="embl">EMBL (m)</option>
|
|
68 <option value="fitch">Fitch (m)</option>
|
|
69 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
|
|
70 <option value="genbank">GENBANK (m)</option>
|
|
71 <option value="gff">GFF (m)</option>
|
|
72 <option value="hennig86">Hennig86 (m)</option>
|
|
73 <option value="ig">Intelligenetics (m)</option>
|
|
74 <option value="jackknifer">Jackknifer (m)</option>
|
|
75 <option value="jackknifernon">Jackknifernon (m)</option>
|
|
76 <option value="mega">Mega (m)</option>
|
|
77 <option value="meganon">Meganon (m)</option>
|
|
78 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
|
|
79 <option value="pir">NBRF (PIR) (m)</option>
|
|
80 <option value="ncbi">NCBI style FASTA (m)</option>
|
|
81 <option value="nexus">Nexus/PAUP (m)</option>
|
|
82 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
|
|
83 <option value="phylip">PHYLIP interleaved (m)</option>
|
|
84 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
|
|
85 <option value="selex">SELEX (m)</option>
|
|
86 <option value="staden">Staden (s)</option>
|
|
87 <option value="strider">DNA strider (m)</option>
|
|
88 <option value="swiss">SwisProt entry (m)</option>
|
|
89 <option value="text">Plain sequence (s)</option>
|
|
90 <option value="treecon">Treecon (m)</option>
|
|
91 </param>
|
|
92 </inputs>
|
|
93 <outputs>
|
|
94 <data format="fasta" name="out_file1" />
|
|
95 </outputs>
|
|
96 <tests>
|
|
97 <test>
|
|
98 <param name="input1" value="2.fasta"/>
|
|
99 <param name="frame" value="1"/>
|
|
100 <param name="table" value="0"/>
|
|
101 <param name="regions" value=""/>
|
|
102 <param name="trim" value="no"/>
|
|
103 <param name="clean" value="no"/>
|
|
104 <param name="alternative" value="no"/>
|
|
105 <param name="out_format1" value="fasta"/>
|
|
106 <output name="out_file1" file="emboss_transeq_out.fasta"/>
|
|
107 </test>
|
|
108 </tests>
|
|
109 <code file="emboss_format_corrector.py" />
|
|
110 <help>
|
|
111
|
|
112 .. class:: warningmark
|
|
113
|
|
114 The input dataset needs to be sequences.
|
|
115
|
|
116 -----
|
|
117
|
|
118 You can view the original documentation here_.
|
|
119
|
|
120 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html
|
|
121 </help>
|
|
122 </tool>
|