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1 <tool id="fixFastq" name="Fix barcodes" version="1.0.0">
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2 <description> generated using Hamming encoding</description>
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3 <command interpreter="python">fixFastq.py $strict $list $fastq $out</command>
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4 <inputs>
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5 <param format="text" name="strict" type="select" value=""/>
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6 <label>Replace unknown barcodes with N</label>
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7 <option value="">No</option>
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8 <option value="-s">Yes</option>
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9 <param format="tabular" name="list" type="data" label="List of barcodes used"/>
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10 <param format="fastqsanger" name="fastq" type="data" label="Barcoded reads"/>
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11 </inputs>
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12 <outputs>
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13 <data format="fastqsanger" name="out"/>
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14 </outputs>
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15 <stdio>
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16 <exit_code range="127" level="fatal" description="Cannot find fixFastq.py"/>
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17 </stdio>
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18 <requirements>
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19 <requirement type="python-module">hamstring</requirement>
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20 </requirements>
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21 <help>
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22 This program accepts a fastqsanger file containing reads that are barcoded on the 5' end using a Hamming7,4 DNA barcode. A list of valid barcodes is checked,
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23 and if the barcode checksum fails the barcode is corrected and checked against this list. If the barcode is not present in the list, it may be replaced
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24 with 'N' to denote ambiguity.
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25 </help>
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26 </tool>
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