| Previous changeset 3:645159bcee2d (2019-06-21) Next changeset 5:a3c4fe6f49ab (2022-06-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6692949aa694102abb64c67d46196a822fcb61bf" |
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modified:
nanoplot.xml test-data/HistogramReadlength.png test-data/NanoPlot-report.html test-data/bam-LogTransformed_HistogramReadlength.svg test-data/bam-report.html |
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| 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 |
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| @@ -1,7 +1,7 @@ <tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1"> <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description> <macros> - <token name="@TOOL_VERSION@">1.25.0</token> + <token name="@TOOL_VERSION@">1.28.2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement> @@ -63,7 +63,6 @@ $filter.percentqual $filter.alength $filter.barcoded - $customization.noN50 $customization.N50 -o '.' ]]></command> @@ -386,12 +385,6 @@ </param> <param type="boolean" - name="noN50" - truevalue="--no-N50" - falsevalue="" - label="Hide the N50 mark in the read length histogram."/> - <param - type="boolean" argument="--N50" truevalue="--N50" falsevalue="" @@ -427,9 +420,8 @@ </section> <section name="customization"> <param name="plots" value="hex,kde"/> - <param name="title" value="My Plot"/> </section> - <output name="output_html" file="NanoPlot-report.html" ftype="html"/> + <output name="output_html" file="NanoPlot-report.html" ftype="html" lines_diff="8" /> <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/> <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/> </test> @@ -448,9 +440,8 @@ <section name="customization"> <param name="color" value="yellow"/> <param name="format" value="svg"/> - <param name="noN50" value="True"/> </section> - <output name="output_html" file="bam-report.html" ftype="html"> + <output name="output_html" file="bam-report.html" ftype="html" lines_diff="16"> <assert_contents> <has_text text="html"/> <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific --> |
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| diff -r 645159bcee2d -r edbb6c5028f5 test-data/HistogramReadlength.png |
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| Binary file test-data/HistogramReadlength.png has changed |
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| 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 |
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| b'@@ -39,6 +39,7 @@\n <p style="margin-left:20px"><a href="#Histogram_of_read_lengths_after_log_transformation">Histogram of read lengths after log transformation</a></p>\n <p style="margin-left:20px"><a href="#Weighted_Histogram_of_read_lengths">Weighted Histogram of read lengths</a></p>\n <p style="margin-left:20px"><a href="#Weighted_Histogram_of_read_lengths_after_log_transformation">Weighted Histogram of read lengths after log transformation</a></p>\n+<p style="margin-left:20px"><a href="#Dynamic_histogram_of_Read_length">Dynamic histogram of Read length</a></p>\n <p style="margin-left:20px"><a href="#Yield_by_length">Yield by length</a></p>\n <p style="margin-left:20px"><a href="#Read_lengths_vs_Average_read_quality_plot_using_hexagonal_bins">Read lengths vs Average read quality plot using hexagonal bins</a></p>\n <p style="margin-left:20px"><a href="#Read_lengths_vs_Average_read_quality_plot_using_a_kernel_density_estimation">Read lengths vs Average read quality plot using a kernel density estimation</a></p>\n@@ -292,7 +293,7 @@\n <h2 id="plots">Plots</h2>\n \n <h3 id="Histogram_of_read_lengths">Histogram of read lengths</h3>\n-<img 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\n <br>\n <br>\n' |
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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 |
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| 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 |
| [ |
| b'@@ -38,6 +38,7 @@\n <p style="margin-left:20px"><a href="#Histogram_of_read_lengths_after_log_transformation">Histogram of read lengths after log transformation</a></p>\n <p style="margin-left:20px"><a href="#Weighted_Histogram_of_read_lengths">Weighted Histogram of read lengths</a></p>\n <p style="margin-left:20px"><a href="#Weighted_Histogram_of_read_lengths_after_log_transformation">Weighted Histogram of read lengths after log transformation</a></p>\n+<p style="margin-left:20px"><a href="#Dynamic_histogram_of_Read_length">Dynamic histogram of Read length</a></p>\n <p style="margin-left:20px"><a href="#Yield_by_length">Yield by length</a></p>\n <p style="margin-left:20px"><a href="#Read_lengths_vs_Average_read_quality_plot_using_dots">Read lengths vs Average read quality plot using dots</a></p>\n <p style="margin-left:20px"><a href="#Read_lengths_vs_Average_read_quality_plot_using_a_kernel_density_estimation">Read lengths vs Average read quality plot using a kernel density estimation</a></p>\n@@ -51,6 +52,7 @@\n <p style="margin-left:20px"><a href="#Percent_identity_vs_Average_Base_Quality_plot_using_a_kernel_density_estimation">Percent identity vs Average Base Quality plot using a kernel density estimation</a></p>\n <p style="margin-left:20px"><a href="#Aligned_read_length_vs_Percent_identity_plot_using_dots">Aligned read length vs Percent identity plot using dots</a></p>\n <p style="margin-left:20px"><a href="#Aligned_read_length_vs_Percent_identity_plot_using_a_kernel_density_estimation">Aligned read length vs Percent identity plot using a kernel density estimation</a></p>\n+<p style="margin-left:20px"><a href="#Dynamic_histogram_of_percent_identity">Dynamic histogram of percent identity</a></p>\n </div>\n <div class="panel panelM"> <h1>NanoPlot report</h1>\n <h2 id="stats0">Summary statistics</h2>\n@@ -68,7 +70,7 @@\n </tr>\n <tr>\n <th>Average percent identity</th>\n- <td>85.3</td>\n+ <td>86.4</td>\n </tr>\n <tr>\n <th>Mean read length</th>\n@@ 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