| Next changeset 1:4c172a4a4c9e (2018-10-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328 |
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added:
nanoplot.xml test-data/HistogramReadlength.jpg test-data/NanoPlot-report.html test-data/NanoStats.txt test-data/NanoStats_post_filtering.txt test-data/alignment.bam test-data/bam-LogTransformed_HistogramReadlength.svg test-data/bam-report.html test-data/reads.fastq.gz |
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| diff -r 000000000000 -r db1eeffba23e nanoplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanoplot.xml Fri Sep 28 19:30:29 2018 -0400 |
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| b'@@ -0,0 +1,468 @@\n+<tool id="nanoplot" name="NanoPlot" version="1.13.0">\n+ <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>\n+ <requirements>\n+ <requirement type="package" version="1.18.2">nanoplot</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+\n+ #set reads_temp = []\n+ #for $i, $f in enumerate($reads.files)\n+ #set $extension = $f.ext\n+ #if $extension == \'fastqsanger\'\n+ #set $extension = \'fastq\'\n+ #end if\n+ ln -s \'$f\' \'./read_${i}.$extension\' &&\n+ $reads_temp.append("read_" + str($i) + "." + str($extension))\n+ #end for\n+\n+ NanoPlot\n+ --$reads.type ${\' \'.join($reads_temp)}\n+\n+ #if $filter.maxlength\n+ --maxlength $filter.maxlength\n+ #end if\n+ #if $filter.minlength\n+ --minlength $filter.minlength\n+ #end if\n+ #if $filter.downsample\n+ --downsample $filter.downsample\n+ #end if\n+ #if $filter.minqual\n+ --minqual $filter.minqual\n+ #end if\n+ #if $filter.readtype\n+ --readtype $filter.readtype\n+ #end if\n+ #if $customization.color\n+ --color $customization.color\n+ #end if\n+ #if $customization.format\n+ --format $customization.format\n+ #end if\n+ #if $customization.plots\n+ --plots ${str($customization.plots).replace(\',\', \' \')}\n+ #end if\n+ $filter.drop_outliers\n+ $filter.loglength\n+ $filter.percentqual\n+ $filter.alength\n+ $filter.barcoded\n+ $customization.noN50\n+ $customization.N50\n+ -o \'.\'\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="reads">\n+ <param name="type" type="select" label="Type of the file(s) to work on">\n+ <option value="fastq" selected="true">fastq</option>\n+ <option value="fasta">fasta</option>\n+ <option value="fastq_rich">fastq_rich</option>\n+ <option value="fastq_minimal">fastq_minimal</option>\n+ <option value="summary">summary</option>\n+ <option value="bam">bam</option>\n+ <option value="cram">cram</option>\n+ </param>\n+ <when value="fastq">\n+ <param\n+ type="data"\n+ argument="--fastq"\n+ name="files"\n+ format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"\n+ multiple="true"/>\n+ </when>\n+ <when value="fasta">\n+ <param\n+ type="data"\n+ argument="--fasta"\n+ name="files"\n+ format="fasta,fasta.gz,vcf_bgzip"\n+ multiple="true"/>\n+ </when>\n+ <when value="fastq_rich">\n+ <param\n+ type="data"\n+ argument="--fastq_rich"\n+ name="files"\n+ format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"\n+ multiple="true"/>\n+ </when>\n+ <when value="fastq_minimal">\n+ <param\n+ type="data"\n+ argument="--fastq_minimal"\n+ name="files"\n+ format="fastq,fastq.gz,fastq.bz2,vcf_bgzip"\n+ multiple="true"/>\n+ </when>\n+ <when value="summary">\n+ <param\n+ type="data"\n+ argument="--summary"\n+ name="files"\n+ format="txt,zip"\n+ multiple="true"/>\n+ </when>\n+ <when value="bam">\n+ <param\n+ '..b'label="${tool.name} on ${on_string}: NanoStats post filtering"/>\n+ <data name="read_length" format="png" from_work_dir="HistogramReadlength.*" label="${tool.name} on ${on_string}: Histogram Read Length ">\n+ <change_format>\n+ <when input="customization.format" value="jpg" format="jpg"/>\n+ <when input="customization.format" value="svg" format="svg"/>\n+ </change_format>\n+ </data>\n+ <data name="log_read_length" format="png" from_work_dir="LogTransformed_HistogramReadlength.*" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length ">\n+ <change_format>\n+ <when input="customization.format" value="jpg" format="jpg"/>\n+ <when input="customization.format" value="svg" format="svg"/>\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="reads">\n+ <param name="type" value="fastq_rich"/>\n+ <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>\n+ </conditional>\n+ <section name="filter">\n+ <param name="downsample" value="800"/>\n+ </section>\n+ <section name="customization">\n+ <param name="plots" value="hex,kde"/>\n+ <param name="title" value="My Plot"/>\n+ <param name="format" value="jpg"/>\n+ </section>\n+ <output name="output_html" file="NanoPlot-report.html" ftype="html"/>\n+ <output name="nanostats" file="NanoStats.txt" ftype="txt"/>\n+ <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>\n+ <output name="read_length" file="HistogramReadlength.jpg" ftype="jpg" compare="sim_size" delta="30000"/>\n+ </test>\n+ <test>\n+ <conditional name="reads">\n+ <param name="type" value="bam"/>\n+ <param name="files" value="alignment.bam" ftype="bam"/>\n+ </conditional>\n+ <section name="filter">\n+ <param name="maxlength" value="2000"/>\n+ <param name="minlenght" value="1000"/>\n+ </section>\n+ <section name="customization">\n+ <param name="color" value="yellow"/>\n+ <param name="format" value="svg"/>\n+ <param name="noN50" value="True"/>\n+ </section>\n+ <output name="output_html" file="bam-report.html" ftype="html" compare="sim_size" delta="50000"/>\n+ <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>\n+ </test>\n+\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\n+ **What it does**\n+\n+ NanoPlot_ is a plotting tool for long read sequencing data and alignments written by `Wouter De Coster`_\n+\n+ .. _NanoPlot: https://github.com/wdecoster/NanoPlot\n+ .. _`Wouter De Coster`: https://github.com/wdecoster\n+\n+ **Input**\n+\n+ NanoPlot requires 1 or more files as input. They can either be fastq (can be generated\n+ by albacore, guppy or MinKNOW containing additional information), fasta, sorted bam,\n+ sorted cram or sequencing summary.\n+\n+ **Output**\n+\n+ NanoPlot produces different number of plots depending on the data and customizations.\n+ A detailed view can be seen on here_. Additionally a file showing the statistics\n+ is generated.\n+\n+ .. _here: https://github.com/wdecoster/NanoPlot#plots-generated\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title =\n+ {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url =\n+ {https://github.com/wdecoster/NanoPlot}, }</citation>\n+ <citation type="doi">10.1093/bioinformatics/bty149</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r db1eeffba23e test-data/HistogramReadlength.jpg |
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| Binary file test-data/HistogramReadlength.jpg has changed |
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| diff -r 000000000000 -r db1eeffba23e test-data/NanoPlot-report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoPlot-report.html Fri Sep 28 19:30:29 2018 -0400 |
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| b'@@ -0,0 +1,362 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <style>\n+ table, th, td {\n+ text-align: left;\n+ padding: 2px;\n+ /* border: 1px solid black;\n+ border-collapse: collapse; */\n+ }\n+ h2 {\n+ line-height: 0pt;\n+ }\n+ .panel {\n+ display: inline-block;\n+ background: #ffffff;\n+ min-height: 100px;\n+ box-shadow:0px 0px 5px 5px #C9C9C9;\n+ -webkit-box-shadow:2px 2px 5px 5x #C9C9C9;\n+ -moz-box-shadow:2px 2px 5px 5px #C9C9C9;\n+ margin: 10px;\n+ padding: 10px;\n+ }\n+ .panelC {\n+ float: left\n+ }\n+ .panelM {\n+ float: left\n+ }\n+ </style>\n+ <title>NanoPlot Report</title>\n+ </head><body>\n+<div class="panel panelC">\n+<p><strong><a href="#stats0">Summary Statistics prior to filtering</a></strong></p>\n+<p><strong><a href="#stats1">Summary Statistics after filtering</a></strong></p>\n+<p><strong><a href="#plots">Plots</a></strong></p>\n+<p style="margin-left:20px"><a href="#Histogram_of_read_lengths">Histogram of read lengths</a></p>\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="#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+<p style="margin-left:20px"><a href="#Number_of_reads_generated_per_channel">Number of reads generated per channel</a></p>\n+<p style="margin-left:20px"><a href="#Cumulative_yield">Cumulative yield</a></p>\n+<p style="margin-left:20px"><a href="#Cumulative_yield">Cumulative yield</a></p>\n+<p style="margin-left:20px"><a href="#Number_of_reads_over_time">Number of reads over time</a></p>\n+<p style="margin-left:20px"><a href="#Number_of_active_pores_over_time">Number of active pores over time</a></p>\n+<p style="margin-left:20px"><a href="#Violin_plot_of_read_lengths_over_time">Violin plot of read lengths over time</a></p>\n+<p style="margin-left:20px"><a href="#Violin_plot_of_quality_over_time">Violin plot of quality over time</a></p>\n+</div>\n+<div class="panel panelM"> <h1>NanoPlot report</h1>\n+<h2 id="stats0">Summary statistics prior to filtering</h2>\n+\n+<table>\n+\n+<tr></tr>\n+<tr>\n+\t<td colspan="2"><b>General summary:</b></td>\n+</tr>\n+<tr>\n+\t<td>Active channels:</td><td>169</td>\n+</tr>\n+<tr>\n+\t<td>Mean read length:</td><td>23212.6</td>\n+</tr>\n+<tr>\n+\t<td>Mean read quality:</td><td>10.1</td>\n+</tr>\n+<tr>\n+\t<td>Median read length:</td><td>9390.0</td>\n+</tr>\n+<tr>\n+\t<td>Median read quality:</td><td>10.3</td>\n+</tr>\n+<tr>\n+\t<td>Number of reads:</td><td>371</td>\n+</tr>\n+<tr>\n+\t<td>Read length N50:</td><td>60395</td>\n+</tr>\n+<tr>\n+\t<td>Total bases:</td><td>8611871</td>\n+</tr>\n+\n+<tr></tr>\n+<tr>\n+\t<td colspan="2"><b>Number, percentage and megabases of reads above quality cutoffs</b></td>\n+</tr>\n+<tr>\n+\t<td>>Q5:</td><td>371 (100.0%) 8.6Mb</td>\n+</tr>\n+<tr>\n+\t<td>>Q7:</td><td>371 (100.0%) 8.6Mb</td>\n+</tr>\n+<tr>\n+\t<td>>Q10:</td><td>207 (55.8%) 4.7Mb</td>\n+</tr>\n+<tr>\n+\t<td>>Q12:</td><td>49 (13.2%) 0.9Mb</td>\n+</tr>\n+<tr>\n+\t<td>>Q15:</td><td>0 (0.0%) 0.0Mb</td>\n+</tr>\n+\n+<tr></tr>\n+<tr>\n+\t<td colspan="2"><b>Top 5 highest mean basecall quality scores and their read lengths</b><'..b'Ts3LkTjz/%2BOG666SbExsbCbrfjxhtv9HaAqWF4qXuQ27t3LzZt2oTKykoMGjSIl7MHuaqqKqxevRqvvfYacnNz%2Becd5L755hts2bIF58%2BfR//%2B/Xl8QRCorq7GjBkzMGzYMO%2BJ%2B3/84x%2Bxb98%2BTJgwAQcOHEDXrl29eze5xNk4DD9EQUSSJHzxxRdwuVw%2BZzsRkRiqqqpw5513YujQoRg1ahQAIDc3F6WlpSguLsbLL7%2BM9u3bc3mzibjnhyiIaDQa7/3biEg8RqMRt99%2BO5YsWYKjR4/i1KlTKC8vx9KlSzF16lQcPHgQ7du3V7pM4TH8EBERqUjfvn1ht9uxdetWJCUlYfr06QDqgpHRaATAi1aaisteREREKvfOO%2B9g2bJlWLZsmfd2FtR43ClFRESkYuvXr8eKFSuwePFiBh8/YeeHiIhIxY4dO4aamhrExsYqXUrQYPghIiKikMJlLyIiIgopDD9EREQUUhh%2BiIiIKKQw/BAREVFIYfghIiKikMLwQ0RERCGF4YcoiK1evRputxtff/31VX/t%2BfPnkZubi%2B3bt8tQmf%2BVlpbC7XZj9erVDXr%2Bjh07kJqaiqNHj3of6927NyZOnChXibI5deoUMjIysGHDBqVLIRICww8RXdb58%2BeRl5eHTz/9VOlS/E6SJMybNw%2BjRo1CQkKC0uU0mcPhwJ133omFCxeiqqpK6XKIVI/hh4gCqrq6GjU1NYrWUFRUhD179mDcuHGK1vF7zp8/3%2BDnjhkzBkePHsUHH3wgY0VEwYHhhyjEPProo%2BjSpQt%2B%2BOEH5OTkoEuXLsjOzsb8%2BfO9XYPS0lJkZWUBAPLy8uB2u%2BF2u/Hoo496xykpKcHUqVORlZWF1NRU9O/fHytWrPCZa/v27XC73VizZg3mz5%2BPnj17Ii0tDfv374fb7caqVasuqW/Tpk1wu93YuHEjAOCHH37A9OnT0bdvX3Tq1Ak9e/bEfffdh3379jX6e7By5UqkpaWhVatWl/18UVERhg0bhvT0dPTr1w9vvfXWJc/57rvvMGnSJGRmZiItLQ1DhgxBfn6%2Bz3Pqlx1LS0t9Hq//vvx6SXH8%2BPEYNGgQPvvsM4wZMwadOnXCY489BgDYunUrxo8fj%2Buuuw7p6eno1asX7r//fp9wFBUVhe7du%2BPNN99s9PeFKFTolS6AiAKvuroakyZNwq233oq77roLn332GZYuXQqbzYYpU6YgOjoaL730Eu655x7ceuutGDlyJADA5XIBAPbv348xY8YgLi4OjzzyCJo1a4ZPPvkEc%2BfOxYkTJzBlyhSf%2BRYvXozOnTvjqaeeglarRWxsLDp06IDVq1d7x66Xn5%2BPyMhIZGdnAwDKy8vhdDoxdepUuFwunDp1Cvn5%2BRg1ahTy8/OvGGCupKqqClu3br1i1%2Bfbb7/FggULkJOTg6ioKKxatQozZsxAUlISMjMzAQAHDx7EmDFjEBkZiRkzZiAiIgJr167Fo48%2BimPHjiEnJ%2BeqaqpXUVGBadOm4Z577sGf/vQnaLValJaWYuLEicjIyMDTTz%2BN8PBwlJWVobi4GNXV1bBYLN6vv/baa7F48WKcPn0a4eHhjaqBKBQw/BCFoOrqatx///3o378/ACArKwu7d%2B/GunXrMGXKFBiNRnTs2BEAEBsbi86dO/t8/TPPPAOr1YqVK1fCZrMBAK6//npUVVXhhRdewPjx4%2BFwOLzPb9GiBf72t7/5jDF8%2BHDMnTsXhw4dQnJyMoC6jbsbN27EuHHjoNfXvT1lZmZ6QwcA1NbWIjs7G4MGDcK//vUvTJ8%2B/ape%2B7fffosLFy54X9/FTpw4gZUrVyI%2BPt47/7Zt21BQUOCtIy8vD9XV1Xj99dcRFxcHAMjOzsbp06fx97//HWPGjIHdbr%2BqugDg5MmTWLJkibfrBgAffPABKisr8fDDD6Ndu3bexwcPHnzJ13fs2BEejwe7du3CDTfccNXzE4UKLnsRhSCNRoPevXv7POZ2u/Hjjz/%2B7tdWVlZi27ZtuPnmm2E2m1FTU%2BP974YbbkBlZSV27drl8zV9%2B/a9ZJzBgwfDaDT6LBWtW7cOVVVVGD58uPexmpoaPP/88xgwYABSU1PRoUMHpKamoqSkBAcOHLjal47y8nIAv3SxLta%2BfXtv8AEAk8mEli1b%2Bnxvtm3bhqysLG/wqTds2DCcP38eX3zxxVXXBdRtXP518Kmvx2Aw4IknnkB%2Bfj6OHDlyxa%2Bvf01lZWWNmp8oVLDzQxSCLBYLTCaTz2NGoxGVlZW/%2B7UnT55ETU0Nli9fjuXLl1/2OSdOnPD5uFmzZpc8x%2Bl0onfv3lizZg0eeOAB6HQ65OfnIz09HW3atPE%2Bb/78%2BVixYgVycnKQmZkJh8MBjUaDxx9/vEH1XuzChQsAcMnr/3VdF7v4e3Py5MnLvqbo6Gjv5xvjcmO2aNECr776Kl566SXMnj0b586dQ/PmzTF%2B/HjccccdPs%2Btf02N%2Bb4QhRKGHyK6KuHh4dDpdBgyZAhuu%2B22yz4nMTHR52ONRnPZ5w0fPhzvv/8%2BNm/ejPj4eHz99deYNWuWz3PWrl2LoUOH4qGHHvJ5/MSJE43a1xIREQGgbomtsZxOJyoqKi55vL6rVD9HfRi5%2BPLzi8NhvSt9nzIyMpCRkYHa2lrs3r0by5cvx7x58xAVFYWBAwd6n1f/murnJ6LLY/ghossyGo0AfumU1LNYLLjuuuuwd%2B9euN1u7/Mao0ePHoiJicHq1asRFxcHk8mEQYMG%2BTxHo9HAYDD4PPbxxx%2BjrKwMSUlJVz1nSkoKAODw4cONrjsrKwsffvghysrKEBMT4338nXfegcVi8e6Rqj9DaN%2B%2BfT4bswsLCxs1r06nQ6dOndCqVSsUFBRgz549PuGnfkms/jUS0eUx/BDRZdlsNiQkJGDjxo3IysqCw%2BFAREQEEhMTMWPGDNx2220YO3Ys/vCHPyAhIQFnz57F4cOHUVhYiNdff71Bc%2Bh0OgwdOhT/%2BMc/YLPZcPPNN1%2ByUbhXr17eq7rcbjf27NmDl19%2BGbGxsY16XbGxsWjevDm%2B/PLLRn09AEyePBkfffQRbr/9dkyePBkOhwMFBQX4%2BOOPMW3aNO9rSEtLQ3JyMhYuXIja2lqEh4djw4YN%2BPzzzxs818qVK7Ft2zb06tULcXFxqKysxNtvvw0A6N69u89zv/zySzidTrjd7ka/NqJQwPBDRFf09NNPY%2BHChZg0aRKqqqowbNgwzJ8/H61bt8bq1auxdOlSLFmyBMePH4fdbkdSUpL3EvWGGj58OJYtW4bjx49jxIgRl3x%2BxowZ0Ov1eOGFF3Du3Dl06NABubm5ePbZZxv9ugYPHowVK1agqqqqUZ2rVq1a4c0338TixYsxe/ZsXLhwASkpKXjmmWd8NmvrdDo8//zzmDNnDmbOnAmj0YiBAwfiySefxL333tugudq3b4/NmzcjNzcXFRUVCAsLQ9u2bfHcc8%2BhR48e3udJkoTCwkIMHjz4istnRFRHI0mSpHQRRESBVFZWhj59%2BmDhwoUYMGCA0uX4xdatW3HXXXdh3bp1XPYi%2Bh281J2IQk5MTAzuuOMOPPfcc/B4PEqX4xdLly7FiBEjGHyIGoDLXkQUkiZNmgSLxYKysrJLzusRzalTp3Dttdde8eo7IvLFZS8iIiIKKVz2IiIiopDC8ENEREQhheGHiIiIQgrDDxEREYUUhh8iIiIKKQw/REREFFIYfoiIiCikMPwQERFRSPk/%2Be7duURrbLUAAAAASUVORK5CYII%3D">\n+\n+<br>\n+<br>\n+<br>\n+<br></div></body></html>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r db1eeffba23e test-data/NanoStats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoStats.txt Fri Sep 28 19:30:29 2018 -0400 |
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| @@ -0,0 +1,27 @@ +General summary: +Active channels: 169 +Mean read length: 23212.6 +Mean read quality: 10.1 +Median read length: 9390.0 +Median read quality: 10.3 +Number of reads: 371 +Read length N50: 60395 +Total bases: 8611871 +Number, percentage and megabases of reads above quality cutoffs +>Q5: 371 (100.0%) 8.6Mb +>Q7: 371 (100.0%) 8.6Mb +>Q10: 207 (55.8%) 4.7Mb +>Q12: 49 (13.2%) 0.9Mb +>Q15: 0 (0.0%) 0.0Mb +Top 5 highest mean basecall quality scores and their read lengths +1: 13.3 (6333) +2: 13.1 (5448) +3: 12.9 (27834) +4: 12.8 (20351) +5: 12.8 (97730) +Top 5 longest reads and their mean basecall quality score +1: 393431 (10.6) +2: 341725 (11.8) +3: 320662 (8.0) +4: 226843 (9.1) +5: 221901 (10.0) |
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| diff -r 000000000000 -r db1eeffba23e test-data/NanoStats_post_filtering.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NanoStats_post_filtering.txt Fri Sep 28 19:30:29 2018 -0400 |
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| @@ -0,0 +1,27 @@ +General summary: +Active channels: 169 +Mean read length: 23212.6 +Mean read quality: 10.1 +Median read length: 9390.0 +Median read quality: 10.3 +Number of reads: 371 +Read length N50: 60395 +Total bases: 8611871 +Number, percentage and megabases of reads above quality cutoffs +>Q5: 371 (100.0%) 8.6Mb +>Q7: 371 (100.0%) 8.6Mb +>Q10: 207 (55.8%) 4.7Mb +>Q12: 49 (13.2%) 0.9Mb +>Q15: 0 (0.0%) 0.0Mb +Top 5 highest mean basecall quality scores and their read lengths +1: 13.3 (6333) +2: 13.1 (5448) +3: 12.9 (27834) +4: 12.8 (20351) +5: 12.8 (97730) +Top 5 longest reads and their mean basecall quality score +1: 393431 (10.6) +2: 341725 (11.8) +3: 320662 (8.0) +4: 226843 (9.1) +5: 221901 (10.0) |
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| diff -r 000000000000 -r db1eeffba23e test-data/bam-LogTransformed_HistogramReadlength.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam-LogTransformed_HistogramReadlength.svg Fri Sep 28 19:30:29 2018 -0400 |
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| diff -r 000000000000 -r db1eeffba23e test-data/bam-report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam-report.html Fri Sep 28 19:30:29 2018 -0400 |
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| b'@@ -0,0 +1,401 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <style>\n+ table, th, td {\n+ text-align: left;\n+ padding: 2px;\n+ /* border: 1px solid black;\n+ border-collapse: collapse; */\n+ }\n+ h2 {\n+ line-height: 0pt;\n+ }\n+ .panel {\n+ display: inline-block;\n+ background: #ffffff;\n+ min-height: 100px;\n+ box-shadow:0px 0px 5px 5px #C9C9C9;\n+ -webkit-box-shadow:2px 2px 5px 5x #C9C9C9;\n+ -moz-box-shadow:2px 2px 5px 5px #C9C9C9;\n+ margin: 10px;\n+ padding: 10px;\n+ }\n+ .panelC {\n+ float: left\n+ }\n+ .panelM {\n+ float: left\n+ }\n+ </style>\n+ <title>NanoPlot Report</title>\n+ </head><body>\n+<div class="panel panelC">\n+<p><strong><a href="#stats0">Summary Statistics prior to filtering</a></strong></p>\n+<p><strong><a href="#stats1">Summary Statistics after filtering</a></strong></p>\n+<p><strong><a href="#plots">Plots</a></strong></p>\n+<p style="margin-left:20px"><a href="#Histogram_of_read_lengths">Histogram of read lengths</a></p>\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="#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+<p style="margin-left:20px"><a href="#Aligned_read_lengths_vs_Sequenced_read_length_plot_using_dots">Aligned read lengths vs Sequenced read length plot using dots</a></p>\n+<p style="margin-left:20px"><a href="#Aligned_read_lengths_vs_Sequenced_read_length_plot_using_a_kernel_density_estimation">Aligned read lengths vs Sequenced read length plot using a kernel density estimation</a></p>\n+<p style="margin-left:20px"><a href="#Read_mapping_quality_vs_Average_basecall_quality_plot_using_dots">Read mapping quality vs Average basecall quality plot using dots</a></p>\n+<p style="margin-left:20px"><a href="#Read_mapping_quality_vs_Average_basecall_quality_plot_using_a_kernel_density_estimation">Read mapping quality vs Average basecall quality plot using a kernel density estimation</a></p>\n+<p style="margin-left:20px"><a href="#Read_length_vs_Read_mapping_quality_plot_using_dots">Read length vs Read mapping quality plot using dots</a></p>\n+<p style="margin-left:20px"><a href="#Read_length_vs_Read_mapping_quality_plot_using_a_kernel_density_estimation">Read length vs Read mapping quality plot using a kernel density estimation</a></p>\n+<p style="margin-left:20px"><a href="#Percent_identity_vs_Average_Base_Quality_plot_using_dots">Percent identity vs Average Base Quality plot using dots</a></p>\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+</div>\n+<div class="panel panelM"> 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No newline at end of file\n' |
| b |
| diff -r 000000000000 -r db1eeffba23e test-data/reads.fastq.gz |
| b |
| Binary file test-data/reads.fastq.gz has changed |
