Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

comparison JunctionDiff-vs-background.xml @ 0:1209f18a5a83 draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 05:01:15 -0400
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-1:000000000000 0:1209f18a5a83
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