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