Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

comparison JunctionDiff-vs-background.xml @ 2:885ba15c2564 draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 05:45:16 -0400
parents 1209f18a5a83
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1:1c6710924e80 2:885ba15c2564
1 <tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.6"> 1 <tool id="t-vs-vnormal_junctions" name="Virtual Normal Correction SVs" version="1.8">
2 <description> Filter SVs based on presence in VN set </description> 2 <description> Filter SVs based on presence in VN set </description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.7">cgatools</requirement> 5 <requirement type="package" version="1.7">cgatools</requirement>
6 </requirements> 6 </requirements>
7 7
8 <command interpreter="bash"> 8 <command interpreter="bash">
9 JunctionDiff-vs-background.sh 9 JunctionDiff-vs-background.sh
10 --variants $variants 10 --variants $variants
11 --reference ${reference.fields.reference_crr_cgatools} 11 --reference ${reference.fields.reference_crr_cgatools}
12 #if $virtnorm.VNset == "diversity" 12 --VN_junctions ${reference.fields.VN_genomes_junctionfile_list}${VNset}
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 13 --cgatools_binary cgatools
18 --outputfile_filtered $output_filtered 14 --outputfile_filtered $output_filtered
19 --scoreThresholdA $scoreThresholdA 15 --scoreThresholdA $scoreThresholdA
20 --scoreThresholdB $scoreThresholdB 16 --scoreThresholdB $scoreThresholdB
21 --distance $distance 17 --distance $distance
22 --minlength $minlength 18 --minlength $minlength
23 </command> 19 </command>
24 20
25 <inputs> 21 <inputs>
22 <param name="variants" type="data" format="tabular" label="CG Junctions file"/>
23
26 <!--select build--> 24 <!--select build-->
27 <param name="reference" type="select" label="Select Build"> 25 <param name="reference" type="select" label="Select Build">
28 <options from_data_table="virtual_normal_correction" /> 26 <options from_data_table="virtual_normal_correction" />
29 <filter type="data_meta" ref="variants" key="dbkey" column="0" />
30 </param> 27 </param>
31 <conditional name="virtnorm" > 28
32 <param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples"> 29 <param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples, for hg18 54 genomes will be used.">
33 <option value="diversity" selected="true"> CG Diversity Panel and trios (54 Genomes) (hg18/hg19) </option> 30 <option value="46_diversity.txt" > CG Diversity Panel (46 Genomes) </option>
34 <option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option> 31 <option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
32 <option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
33 <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
35 </param> 34 </param>
36 </conditional> 35
37 <param name="variants" type="data" format="tabular" label="CG Junctions file"/> 36
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"/> 37 <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"/> 38 <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."/> 39 <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."/> 40 <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?"> 41 <param name="report" type="select" label="Generate report file?">
46 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> 45 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
47 </inputs> 46 </inputs>
48 47
49 <outputs> 48 <outputs>
50 <data format="tabular" name="output_filtered" label="${fname} Filtered junctions for ${tool.name} on ${on_string}"/> 49 <data format="tabular" name="output_filtered" label="${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 ${on_string}"> 50 <data format="tabular" name="output_report" from_work_dir= "output_reports.tsv" label="${fname} report for ${tool.name} on ${on_string}">
52 <filter> report == "Y" </filter> 51 <filter> report == "Y" </filter>
53 </data> 52 </data>
54 </outputs> 53 </outputs>
55 54
56 <help> 55 <help>
57 **What it does** 56 **What it does**
58 57