|
42
|
1 <?xml version="1.0"?>
|
|
|
2 <tool name="Codon Usage" id="codon_usage" version="0.2.5">
|
|
|
3 <description>for each sequence in a file</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2.7.15">python</requirement>
|
|
|
6 <requirement type="package" version="1.72">biopython</requirement>
|
|
|
7 <requirement type="package" version="0.23.4">pandas</requirement>
|
|
|
8 <requirement type="package" version="1.15.3">numpy</requirement>
|
|
|
9 </requirements>
|
|
|
10
|
|
|
11 <command>
|
|
|
12 <![CDATA[
|
|
|
13 python '$__tool_directory__/codon_usage.py' -i $input -t $input_type -o $output -c $codon_table
|
|
|
14 ]]>
|
|
|
15 </command>
|
|
|
16 <inputs>
|
|
|
17 <param name="input" format="fasta" type="data" label="Source file"/>
|
|
|
18
|
|
|
19 <param name="input_type" type="select" format="text">
|
|
|
20 <label>Indicate the input file format</label>
|
|
|
21 <option value="fasta">Fasta</option>
|
|
|
22 <option value="gbk">gbk</option>
|
|
|
23 </param>
|
|
|
24
|
|
|
25 <param name="codon_table" type="select" format="text">
|
|
|
26 <label>Choose the proper codon table for your organism)</label>
|
|
|
27 <option value="Alternative Flatworm Mitochondrial">"Alternative Flatworm Mitochondrial"</option>
|
|
|
28 <option value="Alternative Yeast Nuclear">"Alternative Yeast Nuclear"</option>
|
|
|
29 <option value="Archaeal">"Archaeal"</option>
|
|
|
30 <option value="Ascidian Mitochondrial">"Ascidian Mitochondrial"</option>
|
|
|
31 <option value="Bacterial">"Bacterial"</option>
|
|
|
32 <option value="Blastocrithidia Nuclear">"Blastocrithidia Nuclear"</option>
|
|
|
33 <option value="Blepharisma Macronuclear">"Blepharisma Macronuclear"</option>
|
|
|
34 <option value="Candidate Division SR1">"Candidate Division SR1"</option>
|
|
|
35 <option value="Chlorophycean Mitochondrial">"Chlorophycean Mitochondrial"</option>
|
|
|
36 <option value="Ciliate Nuclear">"Ciliate Nuclear"</option>
|
|
|
37 <option value="Coelenterate Mitochondrial">"Coelenterate Mitochondrial"</option>
|
|
|
38 <option value="Condylostoma Nuclear">"Condylostoma Nuclear"</option>
|
|
|
39 <option value="Dasycladacean Nuclear">"Dasycladacean Nuclear"</option>
|
|
|
40 <option value="Echinoderm Mitochondrial">"Echinoderm Mitochondrial"</option>
|
|
|
41 <option value="Euplotid Nuclear">"Euplotid Nuclear"</option>
|
|
|
42 <option value="Flatworm Mitochondrial">"Flatworm Mitochondrial"</option>
|
|
|
43 <option value="Gracilibacteria">"Gracilibacteria"</option>
|
|
|
44 <option value="Hexamita Nuclear">"Hexamita Nuclear"</option>
|
|
|
45 <option value="Invertebrate Mitochondrial">"Invertebrate Mitochondrial"</option>
|
|
|
46 <option value="Karyorelict Nuclear">"Karyorelict Nuclear"</option>
|
|
|
47 <option value="Mesodinium Nuclear">"Mesodinium Nuclear"</option>
|
|
|
48 <option value="Mold Mitochondrial">"Mold Mitochondrial"</option>
|
|
|
49 <option value="Mycoplasma">"Mycoplasma"</option>
|
|
|
50 <option value="Pachysolen tannophilus Nuclear">"Pachysolen tannophilus Nuclear"</option>
|
|
|
51 <option value="Peritrich Nuclear">"Peritrich Nuclear"</option>
|
|
|
52 <option value="Plant Plastid">"Plant Plastid"</option>
|
|
|
53 <option value="Protozoan Mitochondrial">"Protozoan Mitochondrial"</option>
|
|
|
54 <option value="Pterobranchia Mitochondrial">"Pterobranchia Mitochondrial"</option>
|
|
|
55 <option value="SGC0">"SGC0"</option>
|
|
|
56 <option value="SGC1">"SGC1"</option>
|
|
|
57 <option value="SGC2">"SGC2"</option>
|
|
|
58 <option value="SGC3">"SGC3"</option>
|
|
|
59 <option value="SGC4">"SGC4"</option>
|
|
|
60 <option value="SGC5">"SGC5"</option>
|
|
|
61 <option value="SGC8">"SGC8"</option>
|
|
|
62 <option value="SGC9">"SGC9"</option>
|
|
|
63 <option value="Scenedesmus obliquus Mitochondrial">"Scenedesmus obliquus Mitochondrial"</option>
|
|
|
64 <option value="Spiroplasma">"Spiroplasma"</option>
|
|
|
65 <option value="Standard">"Standard"</option>
|
|
|
66 <option value="Thraustochytrium Mitochondrial">"Thraustochytrium Mitochondrial"</option>
|
|
|
67 <option value="Trematode Mitochondrial">"Trematode Mitochondrial"</option>
|
|
|
68 <option value="Vertebrate Mitochondrial">"Vertebrate Mitochondrial"</option>
|
|
|
69 <option value="Yeast Mitochondrial">"Yeast Mitochondrial"</option>
|
|
|
70 </param>
|
|
|
71 </inputs>
|
|
|
72
|
|
|
73 <outputs>
|
|
|
74 <data format="tabular" name="output" />
|
|
|
75 </outputs>
|
|
|
76
|
|
|
77 <help>
|
|
|
78 This tool computes codon usage of an annotated genome [preferably Prokaryotes].
|
|
|
79 </help>
|
|
|
80 </tool>
|
