Mercurial > repos > geert-vandeweyer > varamplicnv
diff VarAmpliCNV_CallCNVs.xml @ 1:5c324f9a4e20 draft default tip
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author | geert-vandeweyer |
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date | Fri, 25 Sep 2020 08:30:57 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VarAmpliCNV_CallCNVs.xml Fri Sep 25 08:30:57 2020 +0000 @@ -0,0 +1,96 @@ +<tool id="VarAmpliCNV_CallCNVs" name="Call CNVs" version="0.1.0" > + <requirements> + <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ## make output folder. + mkdir Output + + && + + varAmpliCNV.R + + ## counts object + -i $RData + + ## deduped amplicons. + -b $BedFile + + ## Gene information + -r $RoiFile + + ## GC content + -c $GcFile + + ## genders (if specified) + #if $GenderFile + -s $GenderFile + #end if + + ## output folder + -o Output + + ## variance to remove + -p $VarProp + + ## analysis type + -n $aTypeSelect.aType + + ## thresholds + -d $aTypeSelect.delT + -D $aTypeSelect.dupT + + ]]></command> + <inputs> + <param name="RData" type="data" format="rdata" optional="false" label="Sample Amplicon Counts" help="This file is created by the VarAmpliCNV 'Merge Counts' tool." /> + <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." /> + <param name="RoiFile" type="data" format="bed" optional="false" label="ROI-Amplicon file" help="This file is created by the VarAmpliCNV 'annotate' tool." /> + <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."/> + <param name="GenderFile" type="data" format="txt" optional="true" label="Sample Genders" help="Sample genders for handling X-CNVs. See Documentation for format information"/> + <param name="VarProp" type="float" value="0.8" label="Fraction of Variance to remove during MDS" help="Default: 0.8" /> + <conditional name="aTypeSelect"> + <param name="aType" type="select" label="Analysis Type" help="Use 'Direct' Segmentation (pure CBS), or apply post-segmentation 'AOF' (Amplicon Overlap Filtering)"> + <option value='0'>Direct Segmentation</option> + <option value='1' selected="TRUE">Amplicon Overlap Filtering</option> + </param> + <when value='0'> + <param name="delT" value='-0.5' label="LogR Threshold for Deletions" type='float'/> + <param name="dupT" value="0.5" label="LogR Threshold for Duplications" type='float'/> + </when> + <when value='1'> + <param name="delT" value="-0.2" label="LogR Threshold for Deletions" type='float'/> + <param name="dupT" value="0.38" label="LogR Threshold for Duplications" type='float'/> + </when> + </conditional> + </inputs> + <outputs> + <data name="outfile" format="pdf" label="VarAmpliCNV on ${on_string}: Results" > + <discover_datasets pattern="__designation_and_ext__" directory="Output" visible="true" assign_primary_output="true" /> + </data> + </outputs> + <help> +**VarAmpliCNV : Call CNVs** + +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. + +**Parameters are :** + +* Sample Amplicon Counts (RData) : The result from the 'Merge Counts' tool. It contains a raw sample-by-amplicon count matrix. +* 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. +* 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. +* Amplicon GC Content (txt) : GC-content of individual amplicons, used for count correction. Generated using VarAmpliCNV 'Amplicon GC-Content' tool. +* 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 +* 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. +* 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. +* Thresholds : Set mininal values for LogR-based filtering of the called Segments. + + +**Output files :** + +* Parameter_settings : Overview of set and derived settings + a list of discarded samples +* Plots.Quality_Measures : Quality metrics: coverage, variance by PC, GC-coverage-correlation +* Plots.Results : Gene-based CNV plots for segments passing the filters (if AOF is activated) +* Table.Results.Full : Full CBS results +* Table.Results.Filtered : Filtered CBS results (on LogR). +</help> +</tool>