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annotate cwpair2.xml @ 0:afa47be0dc76 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 17:00:15 -0500
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afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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1 <?xml version="1.0"?>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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2 <tool id="cwpair2" name="CWPair2" version="@WRAPPER_VERSION@.0">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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3 <description>find matched pairs and unmatched orphans</description>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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4 <macros>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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5 <import>cwpair2_macros.xml</import>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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6 </macros>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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7 <expand macro="requirements" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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8 <command>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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9 <![CDATA[
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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10 python $__tool_directory__/cwpair2.py
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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11 #for $i in $input:
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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12 --input "${i}" "${i.hid}"
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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13 #end for
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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14 --up_distance $up_distance
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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15 --down_distance $down_distance
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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16 --method $method
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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17 --binsize $binsize
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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18 --threshold_format $threshold_format_cond.threshold_format
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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19 #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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20 --absolute_threshold $threshold_format_cond.absolute_threshold
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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21 #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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22 --relative_threshold $threshold_format_cond.relative_threshold
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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23 #end if
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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24 --output_files $output_files
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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25 --statistics_output "$statistics_output"
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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26 ]]>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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27 </command>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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28 <inputs>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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29 <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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30 <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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31 <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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32 <param name="method" type="select" label="Method of finding a match">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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33 <option value="mode" selected="True">Mode</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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34 <option value="closest">Closest</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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35 <option value="largest">Largest</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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36 <option value="all">All</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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37 </param>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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38 <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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39 <conditional name="threshold_format_cond">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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40 <param name="threshold_format" type="select" label="Filter using">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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41 <option value="relative_threshold" selected="True">Relative threshold</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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42 <option value="absolute_threshold">Absolute threshold</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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43 </param>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
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44 <when value="relative_threshold">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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45 <param name="relative_threshold" type="float" value="0.0" min="0.0" label="Percentage of the 95 percentile value to filter below" help="Value 0 results in no filtering" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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46 </when>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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47 <when value="absolute_threshold">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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48 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" />
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49 </when>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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50 </conditional>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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51 <param name="output_files" type="select" label="Please select the output you want to have" help="Statistics will always be generated." >
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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52 <option value="all" selected="True">no restrictions (output everything: C,D,F,O,P,MP)</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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53 <option value="matched_pair">matched pairs only (MP)</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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54 <option value="matched_pair_orphan">matched pairs and orphans only (O,MP)</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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55 <option value="matched_pair_orphan_detail">matched pairs, orphans and details only (D,O,MP)</option>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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56 </param>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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57 </inputs>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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58 <outputs>
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59 <data name="statistics_output" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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60 <collection name="H" type="list" label="Statistics Histogram: ${tool.name} on ${on_string}">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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61 <filter>output_files == "all"</filter>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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62 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="H" ext="pdf" visible="false" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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63 </collection>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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64 <collection name="D" type="list" label="Data D: ${tool.name} on ${on_string}">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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65 <filter>output_files in ["all", "matched_pair_orphan_detail"]</filter>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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66 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_D" ext="tabular" visible="false" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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67 </collection>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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68 <collection name="O" type="list" label="Data O: ${tool.name} on ${on_string}">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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69 <filter>output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"]</filter>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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70 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_O" ext="tabular" visible="false" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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71 </collection>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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72 <collection name="MP" type="list" label="Data MP: ${tool.name} on ${on_string}">
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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73 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_MP" ext="gff" visible="false" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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74 </collection>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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75 </outputs>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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76 <tests>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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77 <test>
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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78 <param name="input" value="cwpair2_input1.gff" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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79 <param name="up_distance" value="25" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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80 <param name="down_distance" value="100" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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81 <param name="method" value="all" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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82 <param name="binsize" value="1" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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83 <param name="threshold_format" value="relative_threshold" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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84 <param name="relative_threshold" value="0.0" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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85 <param name="output_files" value="matched_pair" />
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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86 <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
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87 <output_collection name="MP" type="list">
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88 <element name="f0u25d100_on_data_1" file="closest_mp_output1.gff" ftype="gff" compare="contains"/>
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89 <element name="f0u25d100_on_data_1" file="largest_mp_output1.gff" ftype="gff" compare="contains"/>
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90 <element name="f0u25d100_on_data_1" file="mode_mp_output1.gff" ftype="gff" compare="contains"/>
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91 </output_collection>
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92 </test>
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93 <test>
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94 <param name="input" value="cwpair2_input1.gff" />
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95 <param name="up_distance" value="50" />
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96 <param name="down_distance" value="100" />
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97 <param name="method" value="all" />
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98 <param name="binsize" value="1" />
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99 <param name="threshold_format" value="relative_threshold" />
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100 <param name="relative_threshold" value="0.0" />
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101 <param name="output_files" value="all" />
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102 <output name="statistics_output" file="statistics2.tabular" ftype="tabular" />
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103 <output_collection name="H" type="list">
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104 <element name="histogram_C_mode_f0u50d100_on_data_1" file="mode_c_output2.pdf" ftype="pdf" compare="contains" lines_diff="12"/>
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105 <element name="histogram_F_closest_f0u50d100_on_data_1" file="closest_f_output2.pdf" ftype="pdf" compare="contains" lines_diff="12"/>
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106 <element name="histogram_F_largest_f0u50d100_on_data_1" file="largest_f_output2.pdf" ftype="pdf" compare="contains" lines_diff="12"/>
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107 <element name="histogram_F_mode_f0u50d100_on_data_1" file="mode_f_output2.pdf" ftype="pdf" compare="contains" lines_diff="12"/>
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108 <element name="histogram_P_mode_f0u50d100_on_data_1" file="mode_p_output2.pdf" ftype="pdf" compare="contains" lines_diff="12"/>
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109 </output_collection>
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110 <output_collection name="D" type="list">
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111 <element name="data_D_closest_f0u50d100_on_data_1" file="closest_d_output2.tabular" ftype="tabular" compare="comntains"/>
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112 <element name="data_D_largest_f0u50d100_on_data_1" file="largest_d_output2.tabular" ftype="tabular" compare="contains"/>
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113 <element name="data_D_mode_f0u50d100_on_data_1" file="mode_d_output2.tabular" ftype="tabular" compare="contains"/>
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114 </output_collection>
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115 <output_collection name="O" type="list">
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116 <element name="data_O_closest_f0u50d100_on_data_1" file="closest_o_output2.tabular" ftype="tabular" compare="contains"/>
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117 <element name="data_O_largest_f0u50d100_on_data_1" file="largest_o_output2.tabular" ftype="tabular" compare="contains"/>
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118 <element name="data_O_mode_f0u50d100_on_data_1" file="mode_o_output2.tabular" ftype="tabular" compare="contains"/>
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119 </output_collection>
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120 <output_collection name="MP" type="list">
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121 <element name="data_MP_closest_f0u50d100_on_data_1" file="closest_mp_output2.gff" ftype="gff" compare="contains"/>
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122 <element name="data_MP_largest_f0u50d100_on_data_1" file="largest_mp_output2.gff" ftype="gff" compare="contains"/>
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123 <element name="data_MP_mode_f0u50d100_on_data_1" file="mode_mp_output2.gff" ftype="gff" compare="contains"/>
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124 </output_collection>
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125 </test>
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126 </tests>
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127 <help>
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128 **What it does**
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129
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130 CWPair accepts one or more gff files as input and takes the peak location to be the midpoint between the
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131 exclusion zone start and end coordinate (columns D and E). CWPair starts with the highest peak (primary peak)
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132 in the dataset, and then looks on the opposite strand for another peak located within the distance defined by
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133 a combination of the tool's **Distance upstream from a peak to allow a pair** (the distance upstream or 5’ to
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134 the primary peak) and **Distance downstream from a peak to allow a pair** (the distance downstream or 3’ to the
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135 primary peak) parameters. So "upstream" value 30 "downstream" value 20 makes the tool look 30 bp upstream and
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136 20 bp downstream (inclusive). Consequently, the search space would be 51 bp, since it includes the primary peak
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137 coordinate. The use of a negative number changes the direction of the search limits. So, "upstream" -30 and
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138 "downstream" 20 produces an 11 bp downstream search window (20-30 bp downstream, inclusive).
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139
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140 .. image:: $PATH_TO_IMAGES/cwpair2.png
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141
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142 When encountering multiple candidate peaks within the search window, CWPair uses the resolution method defined by
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143 the tool's **Method of finding a match** parameter as follows:
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144
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145
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146 * **mode** - This is an iterative process in which all peak-pair distances within the search window are determined, and the mode calculated. The pair whose distance apart is closest to the mode is then selected.
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147 * **closest** - Pairs the peak that has the closest absolute distance from the primary peak.
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148 * **largest** - Pairs the peak that has the highest tag count.
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149 * **all** - Runs all three methods, producing separate outputs for each.
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150
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151 When considering the candidate peaks for pairing to a primary peak, a tag-count threshold may also be set using
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152 the tool's **Filter using relative/absolute threshold** parameter. A relative threshold determines the tag counts
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153 at the 95th percentile of peak occupancy (i.e. top 5% in terms of tag counts), then uses a tag count threshold at
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154 the specified percentage of this 95th percentile. So if the peak at the 95th percentile has 200 tags, and "relative
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155 threshold" 50 is used, then it will not consider any peak having less than 100 tags.
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156
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157 -----
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158
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159 **Options**
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160
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161 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
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162 * **Distance upstream from a peak to allow a pair** - The maximum distance (inclusive) upstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
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163 * **Distance downstream from a peak to allow a pair** - The maximum distance (inclusive) downstream on the opposite strand from the primary peak to locate another peak, resulting in a pair.
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164 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
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165 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
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166 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
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167
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168 -----
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170 **Output Data Files**
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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172 * **closest/largest/mode MP** - gff file containing the Matched Pairs and includes the peak-pair midpoint coordinate (column D) and the coordinate +1 (column E). The tag count sum is reported in column F, along with the C-W distance in bp in column I.
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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173 * **closest/largest/mode O** - tabular file containing the Orphans (all peaks that are not in pairs).
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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174 * **closest/largest/mode D** - tabular file containing the Details, which lists + and – strand information separately. The start and end represent the lower and higher coordinates of the exclusion zone from GeneTrack, and “Value” is the tag count sum within the exclusion zone. The peak pair midpoint is calculated along with the distance between the two paired peaks (midpoint-to-midpoint or C-W distance).
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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176 **Output Statistics Files**
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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178 * **closest/largest/mode C** - pdf file that provides the frequency distribution of peak pair distances.
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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179 * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode).
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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180 * **closest/largest/mode F** - pdf file that provides the final plots graph.
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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181 * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs).
afa47be0dc76 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit e96df94dba60050fa28aaf55b5bb095717a5f260
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183 </help>
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184 <expand macro="citations" />
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185 </tool>