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1 <tool id="convert_bc_to_binary_RY.py" name="Create binary barcodes" version="0.1.0">
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2 <description>from regular barcodes.</description>
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55
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.66">biopython</requirement>
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6 </requirements>
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7 </xml>
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8 <macros>
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9 <import>macros.xml</import>
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10 </macros>
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11 <expand macro="stdio" />
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12 <version_command>python $__tool_directory__/convert_bc_to_binary_RY.py --version</version_command>
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13 <command interpreter="python"><![CDATA[
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14 convert_bc_to_binary_RY.py
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15 #if $positional_1 and $positional_1 is not None:
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16 $positional_1
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17 #end if
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18 > $default]]></command>
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19 <inputs>
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20 <param label="Fastq file to convert." name="positional_1" type="data" format="fastq"/>
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21 </inputs>
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22 <outputs>
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23 <data hidden="false" name="default" format="fastq"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="positional_1" value="extracted_bcs.fastq"/>
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28 <output name="default" file="converted_bcs.fastq"/>
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29 </test>
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30 </tests>
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31 <help><![CDATA[
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32
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33 **What it does**
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34
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35 This tool converts standard nucleotides to IUPAC nucleotide codes used for binary barcodes.
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36 A and G are converted to nucleotide code R. T, U and C are converted to Y.
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37
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38 **Input**
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39
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40 The input for this tool is a fastq file.
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41
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42 **Output**
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43
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44 This tool produces a single fastq file containing the converted barcodes.
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45
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46 ** References **
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47 ]]></help>
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48 <expand macro="citations" />
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49 </tool>
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