Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author saskia-hiltemann
date Mon, 03 Aug 2015 05:45:16 -0400
parents 1209f18a5a83
children
comparison
equal deleted inserted replaced
1:1c6710924e80 2:885ba15c2564
1 <tool id="t-vs-vnormal" name="Virtual Normal Correction SmallVars" version="1.6"> 1 <tool id="t-vs-vnormal" name="Virtual Normal Correction SmallVars" version="1.7">
2 <description> Filter small variants based on presence in Virtual Normal set </description> 2 <description> Filter small variants based on presence in Virtual Normal 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 TV-vs-background.sh 9 TV-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 $virtnorm.VNset == "diversity": 12 --VN_varfiles "${reference.fields.VN_genomes_varfiles_list}${VNset}"
13 --VN_varfiles ${reference.fields.VN_genomes_varfiles_list}
14 #else
15 --VN_varfiles ${reference.fields.VN_genomes_varfiles_list_1000G}
16 #end if
17 --threshold $threshold 13 --threshold $threshold
18 --thresholdhc $thresholdhc 14 --thresholdhc $thresholdhc
19 --outputfile_all $output_all 15 --outputfile_all $output_all
20 --outputfile_filtered $output_filtered 16 --outputfile_filtered $output_filtered
21 </command> 17 </command>
22 18
23 <inputs> 19 <inputs>
24 <param name="variants" type="data" format="tabular" label="List of Variants as produced by Listvariants program or VCF-2-LV conversion program"/> 20 <param name="variants" type="data" format="tabular" label="List of Variants as produced by Listvariants program or VCF-2-LV conversion program"/>
25 <!--select build--> 21 <!--select build-->
26 <param name="reference" type="select" label="Select Build"> 22 <param name="reference" type="select" label="Select Build">
27 <options from_data_table="virtual_normal_correction" /> 23 <options from_data_table="virtual_normal_correction" />
28 <filter type="data_meta" ref="variants" key="dbkey" column="0" />
29 </param> 24 </param>
30 <conditional name="virtnorm" > 25
26 <!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
31 <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."> 27 <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.">
32 <option value="diversity" > CG Diversity Panel and trios (54 Genomes) </option> 28 <option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option>
33 <option value="thousand" > CG 1000G project genomes (433 Genomes) (hg19 only) </option> 29 <option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
34 </param> 30 <option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
35 </conditional> 31 <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
36 32 </param>
37 <param name="threshold" type="text" value="1" label="Threshold: Filter variants if present in at least this number of the background genomes"/> 33
38 <param name="thresholdhc" type="text" value="10" label="High Confidence Threshold: Label a somatic variant as high-confidence if locus was fully called in at least this many normal genomes" help="Please adjust according to number of normals used and desired stringency. "/> 34 <param name="threshold" type="text" value="1" label="Filter out variants present in at least this number of the virtual normal genomes"/>
35 <param name="thresholdhc" type="text" value="10" label="High Confidence Threshold: Label a somatic variant as high-confidence if locus was fully called in at least this many normal genomes" help="Please adjust according to number of normals used and desired stringency. "/>
39 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional. For example sample name."/> 36 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional. For example sample name."/>
40 <!--<param name="debug" type="select" label="individual level annotations?" help="get a columns per normal sample whether variant was present (only available for fully public normal samples)">
41 <option value="N" > No </option>
42 <option value="Y" > Yes </option>
43 </param>
44 -->
45 </inputs> 37 </inputs>
46 38
47 <outputs> 39 <outputs>
48 <data format="tabular" name="output_all" label="${fname} All variants for ${tool.name} on ${on_string}"/> 40 <data format="tabular" name="output_all" label="All variants for ${tool.name} on ${on_string}"/>
49 <data format="tabular" name="output_filtered" label="${fname} Filtered variants for ${tool.name} on ${on_string}"/> 41 <data format="tabular" name="output_filtered" label="Filtered variants for ${tool.name} on ${on_string}"/>
50 <data format="tabular" name="output_filtered_highconf" label="${fname} High Confidence Filtered variants for ${tool.name} on ${on_string}" from_work_dir="output_filtered_highconf.tsv"/> 42 <data format="tabular" name="output_filtered_highconf" label="${fname} High Confidence Filtered variants for ${tool.name} on ${on_string}" from_work_dir="output_filtered_highconf.tsv"/>
51 <!--<data format="tabular" name="output_filtered" label="${fname} Filtered variants for ${tool.name} on ${on_string}"/> 43
52 <data format="tabular" name="output_expanded" from_work_dir="output_expanded" label="${fname} expanded annotation for ${tool.name} on ${on_string}">
53 <filter> $debug == "Y" </filter>
54 </data>
55 -->
56 </outputs> 44 </outputs>
57 45
58 <help> 46 <help>
59 **What it does** 47 **What it does**
60 48