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1 <?xml version="1.0"?>
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2 <tool name="Codon Usage" id="codon_usage" version="0.2.3">
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3 <description>for each sequence in a file</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.15">python</requirement>
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6 <requirement type="package" version="1.72">biopython</requirement>
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7 <requirement type="package" version="0.23.4">pandas</requirement>
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8 <requirement type="package" version="1.15.3">numpy</requirement>
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9 </requirements>
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10
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11 <command>
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12 <![CDATA[
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13 python '$__tool_directory__/codon_usage.py' -i $input -t $input_type -o $output -c $codon_table
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="input" format="fasta" type="data" label="Source file"/>
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18
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19 <param name="input_type" type="select" format="text">
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20 <label>Indicate the input file format</label>
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21 <option value="fasta">Fasta</option>
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22 <option value="gbk">gbk</option>
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23 </param>
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24
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25 <param name="codon_table" type="select" format="text">
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26 <label>Choose the proper codon table for your organism)</label>
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27 <option value="Archaeal"> Archaeal</option>
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28 <option value="Bacterial">Bacterial</option>
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29 <option value="Standard">Standard</option>
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30 </param>
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31 </inputs>
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32
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33 <outputs>
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34 <data format="tabular" name="output" />
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35 </outputs>
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36
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37 <help>
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38 This tool compute codon usage of an annotated genome [preferably Prokaryotes].
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39 </help>
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40 </tool>
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