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comparison Project_RM/codon_usage_complete.xml @ 0:92d2b0a37086 draft

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author gianmarco_piccinno
date Sun, 09 Dec 2018 06:00:26 -0500
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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="python module">biopython</requirement>
5 <requirement type="python module">pandas</requirement>
6 </requirements>
7
8 <command interpreter="python">codon_usage2.py python -i $input -t $input_type -o $output -c $codon_table</command>
9 <inputs>
10 <param name="input" format="fasta" type="data" label="Source file"/>
11
12 <param name="input_type" type="select" format="text">
13 <label>Indicate the input file format</label>
14 <option value="fasta">Fasta</option>
15 <option value="gbk">gbk</option>
16 <option value="gff">gff</option>
17 </param>
18
19
20
21 </inputs>
22
23
24
25 <outputs>
26 <data format="tabular" name="output" />
27 </outputs>
28
29 <tests>
30 <test>
31 <param name="input" value="fa_gc_content_input.fa"/>
32 <output name="out_file1" file="fa_gc_content_output.txt"/>
33 </test>
34 </tests>
35
36 <help>
37 This tool compute codon usage of an annotated genome [preferably Prokaryotes].
38 </help>
39 </tool>