# HG changeset patch # User iuc # Date 1579478582 18000 # Node ID edbb6c5028f595f8cd108c84aea624da9fc6005f # Parent 645159bcee2def21707f7058aa941b1040f653aa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6692949aa694102abb64c67d46196a822fcb61bf" diff -r 645159bcee2d -r edbb6c5028f5 nanoplot.xml --- a/nanoplot.xml Fri Jun 21 19:13:55 2019 -0400 +++ b/nanoplot.xml Sun Jan 19 19:03:02 2020 -0500 @@ -1,7 +1,7 @@ Plotting suite for Oxford Nanopore sequencing data and alignments - 1.25.0 + 1.28.2 nanoplot @@ -63,7 +63,6 @@ $filter.percentqual $filter.alength $filter.barcoded - $customization.noN50 $customization.N50 -o '.' ]]> @@ -386,12 +385,6 @@ -
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- + diff -r 645159bcee2d -r edbb6c5028f5 test-data/HistogramReadlength.png Binary file test-data/HistogramReadlength.png has changed diff -r 645159bcee2d -r edbb6c5028f5 test-data/NanoPlot-report.html --- a/test-data/NanoPlot-report.html Fri Jun 21 19:13:55 2019 -0400 +++ b/test-data/NanoPlot-report.html Sun Jan 19 19:03:02 2020 -0500 @@ -39,6 +39,7 @@

Histogram of read lengths after log transformation

Weighted Histogram of read lengths

Weighted Histogram of read lengths after log transformation

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Dynamic histogram of Read length

Yield by length

Read lengths vs Average read quality plot using hexagonal bins

Read lengths vs Average read quality plot using a kernel density estimation

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Plots

Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Dynamic histogram of Read length

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Yield by length

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Read lengths vs Average read quality plot using hexagonal bins

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Read lengths vs Average read quality plot using a kernel density estimation

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Number of reads generated per channel

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Cumulative yield

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Cumulative yield

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Number of reads over time

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Number of active pores over time

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Violin plot of read lengths over time

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Violin plot of quality over time

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diff -r 645159bcee2d -r edbb6c5028f5 test-data/bam-LogTransformed_HistogramReadlength.svg --- a/test-data/bam-LogTransformed_HistogramReadlength.svg Fri Jun 21 19:13:55 2019 -0400 +++ b/test-data/bam-LogTransformed_HistogramReadlength.svg Sun Jan 19 19:03:02 2020 -0500 @@ -2,17 +2,17 @@ - + @@ -29,12 +29,40 @@ - - + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - + + + - - - - + + + @@ -145,54 +109,13 @@ - - - - - - - - - - - - - - - - - - - - - + @@ -200,71 +123,24 @@ - - - + + - - - + + + - - - - - - - - - - - - - - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - + - + @@ -505,61 +381,189 @@ - - + - + - + + + + - - + - + - + - - + - + - + - - + - + - + + + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - + + + - + - + - + - - + + - + @@ -913,12 +925,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + + - + diff -r 645159bcee2d -r edbb6c5028f5 test-data/bam-report.html --- a/test-data/bam-report.html Fri Jun 21 19:13:55 2019 -0400 +++ b/test-data/bam-report.html Sun Jan 19 19:03:02 2020 -0500 @@ -38,6 +38,7 @@

Histogram of read lengths after log transformation

Weighted Histogram of read lengths

Weighted Histogram of read lengths after log transformation

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Dynamic histogram of Read length

Yield by length

Read lengths vs Average read quality plot using dots

Read lengths vs Average read quality plot using a kernel density estimation

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Percent identity vs Average Base Quality plot using a kernel density estimation

Aligned read length vs Percent identity plot using dots

Aligned read length vs Percent identity plot using a kernel density estimation

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Dynamic histogram of percent identity

NanoPlot report

Summary statistics

@@ -68,7 +70,7 @@ Average percent identity - 85.3 + 86.4 Mean read length @@ -80,7 +82,7 @@ Median percent identity - 87.3 + 87.9 Median read length @@ -183,7 +185,7 @@

Plots

Histogram of read lengths

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Histogram of read lengths after log transformation

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Weighted Histogram of read lengths

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Weighted Histogram of read lengths after log transformation

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Dynamic histogram of Read length

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Yield by length

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Read lengths vs Average read quality plot using dots

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Read lengths vs Average read quality plot using a kernel density estimation

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Aligned read lengths vs Sequenced read length plot using dots

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Aligned read lengths vs Sequenced read length plot using a kernel density estimation

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Read mapping quality vs Average basecall quality plot using dots

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Read mapping quality vs Average basecall quality plot using a kernel density estimation

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Read length vs Read mapping quality plot using dots

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Read length vs Read mapping quality plot using a kernel density estimation

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Percent identity vs Average Base Quality plot using dots

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Percent identity vs Average Base Quality plot using a kernel density estimation

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Aligned read length vs Percent identity plot using dots

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Aligned read length vs Percent identity plot using a kernel density estimation

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Dynamic histogram of percent identity

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