Mercurial > repos > gianmarco_piccinno > project_rm
comparison codon_usage.xml @ 28:e85a1feaaf38 draft
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| author | fabio |
|---|---|
| date | Wed, 12 Dec 2018 08:12:25 -0500 |
| parents | |
| children | e12061ce9601 |
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| 27:1eb19659ff16 | 28:e85a1feaaf38 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool name="Codon Usage" id="codon_usage" version="0.2.0"> | |
| 3 <description>for each sequence in a file</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="3.6.0">python</requirement> | |
| 6 <requirement type="package" version="1.72">biopython</requirement> | |
| 7 <requirement type="package" version="0.23.4">pandas</requirement> | |
| 8 </requirements> | |
| 9 | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 python '$__tool_directory__/codon_usage.py' -i $input -t $input_type -o $output -c $codon_table | |
| 13 ]]> | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param name="input" format="fasta" type="data" label="Source file"/> | |
| 17 | |
| 18 <param name="input_type" type="select" format="text"> | |
| 19 <label>Indicate the input file format</label> | |
| 20 <option value="fasta">Fasta</option> | |
| 21 <option value="gbk">gbk</option> | |
| 22 </param> | |
| 23 | |
| 24 <param name="codon_table" type="select" format="text"> | |
| 25 <label>Choose the proper codon table for your organism)</label> | |
| 26 <option value="Archaeal"> Archaeal</option> | |
| 27 <option value="Bacterial">Bacterial</option> | |
| 28 <option value="Standard">Standard</option> | |
| 29 </param> | |
| 30 </inputs> | |
| 31 | |
| 32 <outputs> | |
| 33 <data format="tabular" name="output" /> | |
| 34 </outputs> | |
| 35 | |
| 36 <help> | |
| 37 This tool compute codon usage of an annotated genome [preferably Prokaryotes]. | |
| 38 </help> | |
| 39 </tool> |