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1 <tool id="encode" name="encode" version="1.0.0">
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2 <description>encode genotypes for further machine learning analysis</description>
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3 <command interpreter="Rscript">
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4 encode.R $config > ${output1}
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5 </command>
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6
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7 <inputs>
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8 <param name="genotype" type="data"
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9 label="genotype data" help="genotype must be a .csv"
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10 />
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11
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12 <param name="separator" type="text" value="/"
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13 label="separator of the heterozygous" help=" caracter used to separate heterozygous in the genotype"
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14 />
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15
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16 <param name="code" type="text" value="0,1,2"
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17 label="coding schem" help=" method to encode the genotype as minor homozygous/heterozygous/major homozygous. Three numbers separated by comma are expected "
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18 />
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19
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20 <param name="encodedPath" type="text"
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21 label="path to the output file" help= " a .csv extension is automatically added by OGHMA"
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22 />
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23 </inputs>
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24
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25
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26 <configfiles>
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27 <configfile name="config">
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28 ## Desc: this file is sourced in encode wrapper script
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29 ## as means to pass all galaxy params to R
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30 "${genotype}" -> genotype
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31 "${separator}" -> sep
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32 "${code}" -> code
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33 "${encodedPath}" -> out
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34
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35 </configfile>
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36 </configfiles>
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37
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38 <outputs>
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39 <data format="tabular" name="output1" label="encoded data" />
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40 </outputs>
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41
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42 <help>
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43 Takes the genotype and encode them in the desired schem (usually 3 integer like 1/2/3) for minor homozygous/heterozygous/major homozygous. The output is a .csv file that may be use by other tools in the OGHMA workflow.
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44 </help>
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45 </tool> |
