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comparison codon_usage.xml @ 17:cb21772b534a draft

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author gianmarco_piccinno
date Tue, 11 Dec 2018 11:43:26 -0500
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children c51d2aa42d7d
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16:9f79249901b7 17:cb21772b534a
1 <tool id="codon_usage" name="Codon Usage" version="0.1.0">
2 <description>for each sequence in a file</description>
3 <requirements>
4 <requirement type=“package” version=“3.6.0”>python</requirement>
5 <requirement type=“package” version=“1.72”>biopython</requirement>
6 <requirement type=“package” version=“0.23.4”>pandas</requirement>
7 </requirements>
8
9 <command>codon_usage.py -i $input -t $input_type -o $output -c $codon_table</command>
10 <inputs>
11 <param name="input" format="fasta" type="data" label="Source file"/>
12
13 <param name="input_type" type="select" format="text">
14 <label>Indicate the input file format</label>
15 <option value="fasta">Fasta</option>
16 <option value="gbk">gbk</option>
17 </param>
18
19 <param name="codon_table" type="select" format="text">
20 <label>Choose the proper codon table for your organism)</label>
21 <option value="Archaeal"> Archaeal</option>
22 <option value="Bacterial">Bacterial</option>
23 <option value="Standard">Standard</option>
24
25 </param>
26
27 </inputs>
28
29
30
31 <outputs>
32 <data format="tabular" name="output" />
33 </outputs>
34
35 <tests>
36 <test>
37 <param name="input" value="fa_gc_content_input.fa"/>
38 <output name="out_file1" file="fa_gc_content_output.txt"/>
39 </test>
40 </tests>
41
42 <help>
43 This tool compute codon usage of an annotated genome [preferably Prokaryotes].
44 </help>
45 </tool>