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6
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1 <tool id="coords2clnt.py" name="Get crosslinked nucleotides" version="0.1.0">
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2 <description>from full alignments</description>
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56
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3 <requirements>
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58
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4 <requirement type="package" version="2.24">bedtools</requirement>
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5 <requirement type="package" version="0.7.4">pybedtools</requirement>
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6 <requirement type="package" version="0.8.3">pysam</requirement>
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56
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7 </requirements>
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0
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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 <stdio>
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13 <exit_code level="fatal" range="1:"/>
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14 </stdio>
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50
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15 <version_command>python $__tool_directory__/coords2clnt.py --version</version_command>
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0
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16 <command interpreter="python"><![CDATA[coords2clnt.py
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17 #if $positional_1 and $positional_1 is not None:
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18 $positional_1
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19 #end if
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20
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21 > $default]]></command>
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22 <inputs>
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23 <param area="false" label="Alignments in bed format." name="positional_1" type="data" format="bed"/>
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24 </inputs>
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25 <outputs>
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26 <data hidden="false" name="default" format="bed"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="positional_1" value="merged_pcr_dupes.bed"/>
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31 <output name="default" file="merged_pcr_dupes_clnts.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 Given coordinates of the aligned reads, calculate positions of the crosslinked nucleotides.
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36 Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read.
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37
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38 Input:
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6
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39
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0
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40 * bed6 file containing coordinates of aligned reads
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41 * bed6 file containing coordinates of crosslinking events
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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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