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