# HG changeset patch # User iuc # Date 1740830545 0 # Node ID 403825b9349a6dadce1f3255bf4990074af5e29d # Parent ee80db1d39c0b088e9eeb124905579df9a77807e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb diff -r ee80db1d39c0 -r 403825b9349a macros.xml --- a/macros.xml Mon Jan 20 16:37:57 2025 +0000 +++ b/macros.xml Sat Mar 01 12:02:25 2025 +0000 @@ -1,10 +1,10 @@ - 1 - 0.9.11 + 0 + 0.9.12 cnvkit - scikit-learn + samtools @@ -56,13 +56,13 @@ - - - - - - - + + + + + + + @@ -70,7 +70,7 @@ - + @@ -85,7 +85,7 @@ - +
@@ -137,7 +137,7 @@ - + @@ -145,32 +145,32 @@ - - + + - + - + - + - + - + @@ -187,32 +187,32 @@ - - - + + + - + - - + + - + - - - - - - - + + + + + + + diff -r ee80db1d39c0 -r 403825b9349a reference.xml --- a/reference.xml Mon Jan 20 16:37:57 2025 +0000 +++ b/reference.xml Sat Mar 01 12:02:25 2025 +0000 @@ -81,7 +81,7 @@
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@@ -196,7 +196,32 @@ chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth) - + +----- + +**Copy Number Reference Profile (.cnn)** + +Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples. + +.. csv-table:: + :header-rows: 0 + + "chromosome","Genomic chromosome (e.g., chr1, chrX)." + "start","Start position of the bin." + "end","End position of the bin." + "gene","Gene name(s) (if applicable)." + "log2","Reference log2 ratio (typically 0 for diploid regions)." + "depth","Average read depth across control samples." + "spread","Variability (standard deviation) of coverage in controls." + +----- + +**Target Coverage File (e.g., sample.targetcoverage.cnn):** + +- **Columns:** chromosome, start, end, gene, reads (raw read count), depth (reads normalized by bin size). + +- **Purpose:** Captures on-target sequencing depth. + ]]> diff -r ee80db1d39c0 -r 403825b9349a test-data/sample.cnv.vcf --- a/test-data/sample.cnv.vcf Mon Jan 20 16:37:57 2025 +0000 +++ b/test-data/sample.cnv.vcf Sat Mar 01 12:02:25 2025 +0000 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20250120 -##source=CNVkit v0.9.11 +##fileDate=20250203 +##source=CNVkit v0.9.12 ##INFO= ##INFO= ##INFO=