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1 <tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="1.0">
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2 <description>
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <version_command>python merge_pcr_duplicates.py --version</version_command>
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10 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
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11 #if $positional_1 and $positional_1 is not None:
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12 $positional_1
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13 #end if
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14
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15 #if $positional_2 and $positional_2 is not None:
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16 $positional_2
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17 #end if
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18
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19 > $default]]></command>
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20 <inputs>
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21 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
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22 <param area="false" label="fasta barcode library." name="positional_2" type="data" format="fasta"/>
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23 </inputs>
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24 <outputs>
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25 <data format="bed" hidden="false" name="default"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="positional_1" value="pcr_dupes_sorted_2.bed"/>
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30 <param name="positional_2" value="pcr_dupes_randomdict.fa"/>
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31 <output name="default" file="merged_pcr_dupes.bed"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 Merge PCR duplicates according to random barcode library.
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36
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37 Barcodes containing uncalled base 'N' are removed.
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38
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39 Input:
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40 * bed6 file containing alignments with fastq read-id in name field
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41 * fasta library with fastq read-id as sequence ids
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42
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43 Output:
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44 * 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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45
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46 Author: Daniel Maticzka
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47 Copyright: 2015
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48 License: Apache
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49 Email: maticzkd@informatik.uni-freiburg.de
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50 Status: Testing
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>
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