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1 <tool id="codon_usage" name="Codon Usage" version="0.1.0">
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2 <description>for each sequence in a file</description>
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3 <requirements>
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4 <requirement type=“package” version=“1.72”>biopython</requirement>
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5 <requirement type=“package” version=“0.23.4”>pandas</requirement>
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6 </requirements>
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7
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8 <command interpreter="python2">codon_usage.py -i $input -t $input_type -o $output -c $codon_table</command>
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9 <inputs>
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10 <param name="input" format="fasta" type="data" label="Source file"/>
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11
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12 <param name="input_type" type="select" format="text">
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13 <label>Indicate the input file format</label>
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14 <option value="fasta">Fasta</option>
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15 <option value="gbk">gbk</option>
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16 </param>
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17
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18 <param name="codon_table" type="select" format="text">
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19 <label>Choose the proper codon table for your organism)</label>
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20 <option value="Archaeal"> Archaeal</option>
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21 <option value="Bacterial">Bacterial</option>
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22 <option value="Standard">Standard</option>
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23
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24 </param>
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25
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26 </inputs>
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27
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28
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29
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30 <outputs>
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31 <data format="tabular" name="output" />
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32 </outputs>
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33
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34 <tests>
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35 <test>
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36 <param name="input" value="fa_gc_content_input.fa"/>
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37 <output name="out_file1" file="fa_gc_content_output.txt"/>
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38 </test>
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39 </tests>
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40
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41 <help>
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42 This tool compute codon usage of an annotated genome [preferably Prokaryotes].
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43 </help>
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44 </tool>
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