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6
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1 <tool id="extract_bcs.py" name="Extract barcodes" version="1.0.0">
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2 <description>using pattern.</description>
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56
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3 <requirements>
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4 <requirement type="package" version="1.66">biopython</requirement>
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5 </requirements>
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0
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="stdio" />
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50
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10 <version_command>python $__tool_directory__/extract_bcs.py --version</version_command>
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0
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11 <command interpreter="python"><![CDATA[
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12 extract_bcs.py
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13 #if $positional_1 and $positional_1 is not None:
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14 $positional_1
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15 #end if
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16
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17 #if $positional_2 and $positional_2 is not None:
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18 $positional_2
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19 #end if
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20
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5
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21 --bcs $extractedbcs
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22
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0
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23 > $default]]></command>
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24 <inputs>
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25 <param area="false" label="Barcoded sequences." name="positional_1" type="data" format="fastq"/>
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26 <param area="false" label="Pattern of barcode nucleotides starting at 5'-end. X positions will be moved to the header, N positions will be kept." name="positional_2" type="text"/>
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27 </inputs>
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28 <outputs>
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5
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29 <data hidden="false" name="default" format="fastq"/>
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9
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30 <data name="extractedbcs" format="fastq"/>
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0
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="positional_1" value="reads.fastq"/>
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35 <param name="positional_2" value="XXXNNXXX"/>
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5
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36 <output name="default" file="result_original_head.fastq"/>
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9
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37 <output name="extractedbcs" file="extracted_bcs.fastq"/>
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0
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 Exract barcodes from a FASTQ file according to a user-specified pattern.
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42
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43 Author: Daniel Maticzka
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44 Copyright: 2015
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45 License: Apache
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46 Email: maticzkd@informatik.uni-freiburg.de
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47 Status: Testing
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>
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