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1 <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0">
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6
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2 <description>according to random barcode library.</description>
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56
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3 <requirements>
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4 <requirement type="package" version="4.1.0">gnu_awk</requirement>
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5 <requirement type="package" version="8.22">gnu_coreutils</requirement>
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6 <requirement type="package" version="1.0.6">datamash</requirement>
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7 </requirements>
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2
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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__/merge_pcr_duplicates.py --version</version_command>
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13 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
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14 #if $positional_1 and $positional_1 is not None:
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15 $positional_1
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16 #end if
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17
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18 #if $positional_2 and $positional_2 is not None:
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19 $positional_2
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20 #end if
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21
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22 --outfile $default]]></command>
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2
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23 <inputs>
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24 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
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25 <param area="false" label="fastaq barcode library." name="positional_2" type="data" format="fastq"/>
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2
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26 </inputs>
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27 <outputs>
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28 <data format="bed" hidden="false" name="default"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="positional_1" value="pcr_dupes_sorted_2.bed"/>
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33 <param name="positional_2" value="pcr_dupes_randomdict.fastq"/>
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34 <output name="default" file="merged_pcr_dupes.bed"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 Merge PCR duplicates according to random barcode library.
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39
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40 Barcodes containing uncalled base 'N' are removed.
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41
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42 Input::
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43
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44 * bed6 file containing alignments with fastq read-id in name field
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45 * fastq library of random barcodes
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2
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46
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47 Output::
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48
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49 * bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name
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50
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51 Author: Daniel Maticzka
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52 Copyright: 2015
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53 License: Apache
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54 Email: maticzkd@informatik.uni-freiburg.de
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55 Status: Testing
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56 ]]></help>
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57 <expand macro="citations" />
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58 </tool>
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