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comparison codon_switch.xml @ 0:5397da1ef896 draft

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author gianmarco_piccinno
date Tue, 21 May 2019 05:05:15 -0400
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1 <?xml version="1.0"?>
2 <tool name="Codon Switch Tool" id="codon_switch" version="0.2.6">
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_switch.py' -i $input -l $input_type -p $patterns -g $genome -g $genome_type -c $codon_table -f $num_plasmids -m $row_len -d $demonstration -o $output
14 ]]>
15 </command>
16 <inputs>
17 <param name="input" format="genbank" type="data" label="Input plasmid"/>
18
19 <param name="input_type" type="select" format="text">
20 <label>Indicate the input file format.</label>
21 <option value="genbank">genbank</option>
22 </param>
23
24 <param name="patterns" format="txt" type="data" label="Patterns file"/>
25
26 <param name="genome" format="genbank" type="data" label="Input Genome"/>
27
28 <param name="genome_type" type="select" format="text">
29 <label>Indicate the input genome format.</label>
30 <option value="fasta">fasta</option>
31 <option value="genbank">genbank</option>
32 </param>
33
34 <param name="demonstration" type="select" format="text">
35 <label>Demonstration</label>
36 <option value="demonstration">yes</option>
37 <option value="no_demonstration">no</option>
38 </param>
39
40 <param name="num_plasmids" type="select" format="text">
41 <label>Indicate the number of best output plamids.</label>
42 <option value=3>3</option>
43 <option value=7>7</option>
44 </param>
45
46 <param name="row_len" type="select" format="text">
47 <label>Indicate the length of the row in report file.</label>
48 <option value=9>9</option>
49 <option value=27>27</option>
50 </param>
51
52 <param name="codon_table" type="select" format="text">
53 <label>Choose the proper codon table for your organism.</label>
54 <option value="Alternative Flatworm Mitochondrial">"Alternative Flatworm Mitochondrial"</option>
55 <option value="Alternative Yeast Nuclear">"Alternative Yeast Nuclear"</option>
56 <option value="Archaeal">"Archaeal"</option>
57 <option value="Ascidian Mitochondrial">"Ascidian Mitochondrial"</option>
58 <option value="Bacterial">"Bacterial"</option>
59 <option value="Blastocrithidia Nuclear">"Blastocrithidia Nuclear"</option>
60 <option value="Blepharisma Macronuclear">"Blepharisma Macronuclear"</option>
61 <option value="Candidate Division SR1">"Candidate Division SR1"</option>
62 <option value="Chlorophycean Mitochondrial">"Chlorophycean Mitochondrial"</option>
63 <option value="Ciliate Nuclear">"Ciliate Nuclear"</option>
64 <option value="Coelenterate Mitochondrial">"Coelenterate Mitochondrial"</option>
65 <option value="Condylostoma Nuclear">"Condylostoma Nuclear"</option>
66 <option value="Dasycladacean Nuclear">"Dasycladacean Nuclear"</option>
67 <option value="Echinoderm Mitochondrial">"Echinoderm Mitochondrial"</option>
68 <option value="Euplotid Nuclear">"Euplotid Nuclear"</option>
69 <option value="Flatworm Mitochondrial">"Flatworm Mitochondrial"</option>
70 <option value="Gracilibacteria">"Gracilibacteria"</option>
71 <option value="Hexamita Nuclear">"Hexamita Nuclear"</option>
72 <option value="Invertebrate Mitochondrial">"Invertebrate Mitochondrial"</option>
73 <option value="Karyorelict Nuclear">"Karyorelict Nuclear"</option>
74 <option value="Mesodinium Nuclear">"Mesodinium Nuclear"</option>
75 <option value="Mold Mitochondrial">"Mold Mitochondrial"</option>
76 <option value="Mycoplasma">"Mycoplasma"</option>
77 <option value="Pachysolen tannophilus Nuclear">"Pachysolen tannophilus Nuclear"</option>
78 <option value="Peritrich Nuclear">"Peritrich Nuclear"</option>
79 <option value="Plant Plastid">"Plant Plastid"</option>
80 <option value="Protozoan Mitochondrial">"Protozoan Mitochondrial"</option>
81 <option value="Pterobranchia Mitochondrial">"Pterobranchia Mitochondrial"</option>
82 <option value="SGC0">"SGC0"</option>
83 <option value="SGC1">"SGC1"</option>
84 <option value="SGC2">"SGC2"</option>
85 <option value="SGC3">"SGC3"</option>
86 <option value="SGC4">"SGC4"</option>
87 <option value="SGC5">"SGC5"</option>
88 <option value="SGC8">"SGC8"</option>
89 <option value="SGC9">"SGC9"</option>
90 <option value="Scenedesmus obliquus Mitochondrial">"Scenedesmus obliquus Mitochondrial"</option>
91 <option value="Spiroplasma">"Spiroplasma"</option>
92 <option value="Standard">"Standard"</option>
93 <option value="Thraustochytrium Mitochondrial">"Thraustochytrium Mitochondrial"</option>
94 <option value="Trematode Mitochondrial">"Trematode Mitochondrial"</option>
95 <option value="Vertebrate Mitochondrial">"Vertebrate Mitochondrial"</option>
96 <option value="Yeast Mitochondrial">"Yeast Mitochondrial"</option>
97 </param>
98 </inputs>
99
100 <outputs>
101 <data format="tabular" name="output" />
102 </outputs>
103
104 <help>
105 This tool permits codon switch and transversion in targeted regions.
106 </help>
107 </tool>