Mercurial > repos > fabio > new_project_rm
comparison codon_usage.xml @ 0:5b61f1b564b3 draft
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| author | fabio |
|---|---|
| date | Tue, 11 Dec 2018 12:27:52 -0500 |
| parents | |
| children | 71fd72235543 |
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| -1:000000000000 | 0:5b61f1b564b3 |
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| 1 <tool id="codon_usage" name="Codon Usage" version="0.2.0"> | |
| 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>python $__tool_directory__/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 </inputs> | |
| 27 | |
| 28 <outputs> | |
| 29 <data format="tabular" name="output" /> | |
| 30 </outputs> | |
| 31 | |
| 32 <help> | |
| 33 This tool compute codon usage of an annotated genome [preferably Prokaryotes]. | |
| 34 </help> | |
| 35 </tool> |