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1 <tool id="rm_spurious_events.py" name="Remove spurious" version="0.1.0">
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2 <description>crosslinking events</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="8.22">gnu_coreutils</requirement>
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6 <requirement type="package" version="5.18.1">perl</requirement>
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7 </requirements>
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8 </xml>
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0
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9 <macros>
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10 <import>macros.xml</import>
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11 </macros>
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12 <expand macro="stdio" />
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13 <version_command>python $__tool_directory__/rm_spurious_events.py --version</version_command>
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0
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14 <command interpreter="python"><![CDATA[rm_spurious_events.py
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15 #if $positional_1 and $positional_1 is not None:
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16 $positional_1
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17 #end if
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18
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19 #if $threshold and $threshold is not None:
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20 --threshold $threshold
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21 #end if
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22 --outfile $default]]></command>
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0
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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 help="(--threshold)" label="Threshold for spurious event removal." name="threshold" optional="true" type="float" value="0.1"/>
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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="merged_pcr_dupes_spurious.bed"/>
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33 <param name="threshold" value="0.5"/>
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34 <output name="default" file="merged_pcr_dupes_spurious_filtered_thresh05.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 Remove spurious events originating from errors in random sequence tags.
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39
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40 This tool compares all events sharing the same coordinates. Among each group
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41 of events the maximum number of PCR duplicates is determined. All events that
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42 are supported by less than 10 percent of this maximum count 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 crosslinking events with score field set to number of PCR duplicates
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0
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47
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48 Output::
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49
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50 * bed6 file with spurious crosslinking events removed, sorted by fields chrom, start, stop, strand
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0
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51
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52 Author: Daniel Maticzka
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53 Copyright: 2015
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54 License: Apache
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55 Email: maticzkd@informatik.uni-freiburg.de
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56 Status: Testing
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57 ]]></help>
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58 <expand macro="citations" />
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59 </tool>
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