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1 <tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.6">
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2 <description> Filter SVs based on presence in VN set </description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.7">cgatools</requirement>
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6 </requirements>
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7
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8 <command interpreter="bash">
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9 JunctionDiff-vs-background.sh
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10 --variants $variants
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11 --reference ${reference.fields.reference_crr_cgatools}
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12 #if $virtnorm.VNset == "diversity"
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13 --VN_junctions ${reference.fields.VN_genomes_junctionfile_list}
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14 #else
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15 --VN_junctions ${reference.fields.VN_genomes_junctionfile_list_1000G}
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16 #end if
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17 --cgatools_binary cgatools
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18 --outputfile_filtered $output_filtered
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19 --scoreThresholdA $scoreThresholdA
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20 --scoreThresholdB $scoreThresholdB
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21 --distance $distance
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22 --minlength $minlength
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23 </command>
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24
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25 <inputs>
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26 <!--select build-->
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27 <param name="reference" type="select" label="Select Build">
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28 <options from_data_table="virtual_normal_correction" />
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29 <filter type="data_meta" ref="variants" key="dbkey" column="0" />
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30 </param>
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31 <conditional name="virtnorm" >
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32 <param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples">
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33 <option value="diversity" selected="true"> CG Diversity Panel and trios (54 Genomes) (hg18/hg19) </option>
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34 <option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
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35 </param>
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36 </conditional>
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37 <param name="variants" type="data" format="tabular" label="CG Junctions file"/>
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38 <param name="scoreThresholdA" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from input genome"/>
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39 <param name="scoreThresholdB" type="text" value="10" label="scoreThreshold" help="The minimum number of discordant mate pair alignments supporting the junction from background genomes"/>
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40 <param name="distance" type="text" value="200" label="Maximum distance between coordinates of potentially compatible junctions."/>
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41 <param name="minlength" type="text" value="500" label="Minimum deletion junctions length to be included into the difference file."/>
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42 <param name="report" type="select" label="Generate report file?">
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43 <option value="N" selected="true"> No </option>
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44 <option value="Y"> Yes </option>
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45 </param>
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46 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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47 </inputs>
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48
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49 <outputs>
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50 <data format="tabular" name="output_filtered" label="${fname} Filtered junctions for ${tool.name} on ${on_string}"/>
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51 <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on ${on_string}">
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52 <filter> report == "Y" </filter>
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53 </data>
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54 </outputs>
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55
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56 <help>
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57 **What it does**
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58
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59
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60
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61 **Input Files**
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62 Complete Genomics Junctions file
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63
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64 **Output Files**
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65 Junctions remaining after filtering
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66
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67
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68 </help>
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69
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70 </tool>
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71
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72
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