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comparison VarAmpliCNV_CallCNVs.xml @ 1:5c324f9a4e20 draft default tip

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author geert-vandeweyer
date Fri, 25 Sep 2020 08:30:57 +0000
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0:febc6023d37b 1:5c324f9a4e20
1 <tool id="VarAmpliCNV_CallCNVs" name="Call CNVs" version="0.1.0" >
2 <requirements>
3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 ## make output folder.
7 mkdir Output
8
9 &&
10
11 varAmpliCNV.R
12
13 ## counts object
14 -i $RData
15
16 ## deduped amplicons.
17 -b $BedFile
18
19 ## Gene information
20 -r $RoiFile
21
22 ## GC content
23 -c $GcFile
24
25 ## genders (if specified)
26 #if $GenderFile
27 -s $GenderFile
28 #end if
29
30 ## output folder
31 -o Output
32
33 ## variance to remove
34 -p $VarProp
35
36 ## analysis type
37 -n $aTypeSelect.aType
38
39 ## thresholds
40 -d $aTypeSelect.delT
41 -D $aTypeSelect.dupT
42
43 ]]></command>
44 <inputs>
45 <param name="RData" type="data" format="rdata" optional="false" label="Sample Amplicon Counts" help="This file is created by the VarAmpliCNV 'Merge Counts' tool." />
46 <param name="BedFile" type="data" format="bed" optional="false" label="Amplicon BED file (duplicates removed)" help="This file is created by the VarAmpliCNV 'annotate' tool." />
47 <param name="RoiFile" type="data" format="bed" optional="false" label="ROI-Amplicon file" help="This file is created by the VarAmpliCNV 'annotate' tool." />
48 <param name="GcFile" type="data" format="txt" optional="false" label="Amplicon GC content" help="This file is created by the VarAmpliCNV 'Get GC Content' tool."/>
49 <param name="GenderFile" type="data" format="txt" optional="true" label="Sample Genders" help="Sample genders for handling X-CNVs. See Documentation for format information"/>
50 <param name="VarProp" type="float" value="0.8" label="Fraction of Variance to remove during MDS" help="Default: 0.8" />
51 <conditional name="aTypeSelect">
52 <param name="aType" type="select" label="Analysis Type" help="Use 'Direct' Segmentation (pure CBS), or apply post-segmentation 'AOF' (Amplicon Overlap Filtering)">
53 <option value='0'>Direct Segmentation</option>
54 <option value='1' selected="TRUE">Amplicon Overlap Filtering</option>
55 </param>
56 <when value='0'>
57 <param name="delT" value='-0.5' label="LogR Threshold for Deletions" type='float'/>
58 <param name="dupT" value="0.5" label="LogR Threshold for Duplications" type='float'/>
59 </when>
60 <when value='1'>
61 <param name="delT" value="-0.2" label="LogR Threshold for Deletions" type='float'/>
62 <param name="dupT" value="0.38" label="LogR Threshold for Duplications" type='float'/>
63 </when>
64 </conditional>
65 </inputs>
66 <outputs>
67 <data name="outfile" format="pdf" label="VarAmpliCNV on ${on_string}: Results" >
68 <discover_datasets pattern="__designation_and_ext__" directory="Output" visible="true" assign_primary_output="true" />
69 </data>
70 </outputs>
71 <help>
72 **VarAmpliCNV : Call CNVs**
73
74 During CNV calling read counts are normalized over all samples inluced during "count merging", a set fraction of variance is removed and circular binary segmentation is applied to identify CNVs. If specified, a post-processing step is applied to take amplicon size and overlap into account to estimate reliability of the event. Passing CNVs are plotted gene-by-gene.
75
76 **Parameters are :**
77
78 * Sample Amplicon Counts (RData) : The result from the 'Merge Counts' tool. It contains a raw sample-by-amplicon count matrix.
79 * Amplicon BED file (BED) : This is the *exact* BED file provided by HaloPlex for the used library, with duplicates removed using the VarAmpliCNV "Annotate" tool.
80 * ROI file (BED) : This is the *exact* BED file provided by HaloPlex for the used library, with duplicates removed and annotated with gene symbols using the VarAmpliCNV "Annotate" tool.
81 * Amplicon GC Content (txt) : GC-content of individual amplicons, used for count correction. Generated using VarAmpliCNV 'Amplicon GC-Content' tool.
82 * Sample Genders (txt) : Optional. If specified, build gender-specific normalization sets for X and Y chromosomes. Format is tab-separated : SamplenName&lt;tab&gt;M/F/U
83 * Fraction of Variance to Remove : Using an approach similar to Principal component analysis, a preset fraction of noise is removed from the data. Higher values typically result in less CNVs.
84 * Analysis Type : Direct Segmentation applies only CBS and will not plot results. Amplicon Overlap Filtering is a post-processing filter to improve specificity, and will also enable plotting. The full CBS-results are always returned for manual inspection.
85 * Thresholds : Set mininal values for LogR-based filtering of the called Segments.
86
87
88 **Output files :**
89
90 * Parameter_settings : Overview of set and derived settings + a list of discarded samples
91 * Plots.Quality_Measures : Quality metrics: coverage, variance by PC, GC-coverage-correlation
92 * Plots.Results : Gene-based CNV plots for segments passing the filters (if AOF is activated)
93 * Table.Results.Full : Full CBS results
94 * Table.Results.Filtered : Filtered CBS results (on LogR).
95 </help>
96 </tool>