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1 <tool id="VarAmpliCNV_CallCNVs" name="Call CNVs" version="0.1.0" >
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2 <requirements>
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3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 ## make output folder.
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7 mkdir Output
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8
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9 &&
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10
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11 varAmpliCNV.R
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12
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13 ## counts object
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14 -i $RData
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15
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16 ## deduped amplicons.
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17 -b $BedFile
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18
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19 ## Gene information
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20 -r $RoiFile
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21
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22 ## GC content
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23 -c $GcFile
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24
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25 ## genders (if specified)
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26 #if $GenderFile
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27 -s $GenderFile
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28 #end if
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29
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30 ## output folder
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31 -o Output
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32
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33 ## variance to remove
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34 -p $VarProp
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35
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36 ## analysis type
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37 -n $aTypeSelect.aType
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38
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39 ## thresholds
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40 -d $aTypeSelect.delT
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41 -D $aTypeSelect.dupT
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42
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43 ]]></command>
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44 <inputs>
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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." />
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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." />
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47 <param name="RoiFile" type="data" format="bed" optional="false" label="ROI-Amplicon file" help="This file is created by the VarAmpliCNV 'annotate' tool." />
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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."/>
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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"/>
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50 <param name="VarProp" type="float" value="0.8" label="Fraction of Variance to remove during MDS" help="Default: 0.8" />
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51 <conditional name="aTypeSelect">
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52 <param name="aType" type="select" label="Analysis Type" help="Use 'Direct' Segmentation (pure CBS), or apply post-segmentation 'AOF' (Amplicon Overlap Filtering)">
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53 <option value='0'>Direct Segmentation</option>
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54 <option value='1' selected="TRUE">Amplicon Overlap Filtering</option>
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55 </param>
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56 <when value='0'>
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57 <param name="delT" value='-0.5' label="LogR Threshold for Deletions" type='float'/>
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58 <param name="dupT" value="0.5" label="LogR Threshold for Duplications" type='float'/>
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59 </when>
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60 <when value='1'>
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61 <param name="delT" value="-0.2" label="LogR Threshold for Deletions" type='float'/>
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62 <param name="dupT" value="0.38" label="LogR Threshold for Duplications" type='float'/>
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63 </when>
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64 </conditional>
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65 </inputs>
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66 <outputs>
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67 <data name="outfile" format="pdf" label="VarAmpliCNV on ${on_string}: Results" >
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68 <discover_datasets pattern="__designation_and_ext__" directory="Output" visible="true" assign_primary_output="true" />
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69 </data>
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70 </outputs>
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71 <help>
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72 **VarAmpliCNV : Call CNVs**
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73
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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.
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75
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76 **Parameters are :**
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77
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78 * Sample Amplicon Counts (RData) : The result from the 'Merge Counts' tool. It contains a raw sample-by-amplicon count matrix.
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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.
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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.
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81 * Amplicon GC Content (txt) : GC-content of individual amplicons, used for count correction. Generated using VarAmpliCNV 'Amplicon GC-Content' tool.
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82 * Sample Genders (txt) : Optional. If specified, build gender-specific normalization sets for X and Y chromosomes. Format is tab-separated : SamplenName<tab>M/F/U
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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.
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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.
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85 * Thresholds : Set mininal values for LogR-based filtering of the called Segments.
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86
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87
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88 **Output files :**
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89
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90 * Parameter_settings : Overview of set and derived settings + a list of discarded samples
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91 * Plots.Quality_Measures : Quality metrics: coverage, variance by PC, GC-coverage-correlation
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92 * Plots.Results : Gene-based CNV plots for segments passing the filters (if AOF is activated)
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93 * Table.Results.Full : Full CBS results
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94 * Table.Results.Filtered : Filtered CBS results (on LogR).
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95 </help>
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96 </tool>
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