| Previous changeset 4:edbb6c5028f5 (2020-01-19) Next changeset 6:0f1c34698076 (2023-02-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 52e462654477b6acf9a087063d3ddb19f66f8b38 |
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modified:
nanoplot.xml test-data/HistogramReadlength.png test-data/NanoStats.txt test-data/NanoStats_post_filtering.txt |
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| diff -r edbb6c5028f5 -r a3c4fe6f49ab nanoplot.xml --- a/nanoplot.xml Sun Jan 19 19:03:02 2020 -0500 +++ b/nanoplot.xml Thu Jun 16 20:08:15 2022 +0000 |
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| b'@@ -1,38 +1,61 @@\n-<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1">\n+<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1" profile="20.05">\n <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.28.2</token>\n+ <token name="@TOOL_VERSION@">1.36.2</token>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>\n </requirements>\n+ <stdio>\n+ <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />\n+ </stdio>\n <version_command>NanoPlot --version</version_command>\n <command detect_errors="exit_code"><![CDATA[\n+## set TMPDIR if not already set by admin\n+## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`\n+## export TMPDIR=\\${TMPDIR:-\\$_GALAXY_JOB_TMP_DIR};\n+\n #set $myfiles = $mode.reads.files\n-\n #set reads_temp = []\n #if $mode.choice == \'combined\':\n #for $i, $f in enumerate($myfiles)\n- #if $f.ext == "fastqsanger":\n+ #if $f.ext.startswith("fastq"):\n #set $extension = \'fastq\'\n #else\n #set $extension = $f.ext\n #end if\n+ #if $f.ext.endswith(".gz"):\n+ #set $f = $extension + ".gz"\n+ #else if $f.ext.endswith(".bz"):\n+ #set $extension = $extension + "bz2"\n+ #end if\n ln -s \'$f\' \'./read_${i}.$extension\' &&\n+ #if "bam" in $extension\n+ ln -s \'$f.metadata.bam_index\' \'./read_${i}.${extension}.bai\' &&\n+ #end if\n $reads_temp.append("read_" + str($i) + "." + str($extension))\n #end for\n #else\n- #if $myfiles.ext == "fastqsanger":\n+ #if $myfiles.ext.startswith("fastq"):\n #set $extension = \'fastq\'\n #else\n #set $extension = $myfiles.ext\n #end if\n- ln -s \'$mode.reads.files\' \'./read.$extension\' &&\n+ #if $myfiles.ext.endswith(".gz"):\n+ #set $extension = $extension + ".gz"\n+ #else if $myfiles.ext.endswith(".bz"):\n+ #set $extension = $extension + "bz2"\n+ #end if\n+ ln -s \'$myfiles\' \'./read.$extension\' &&\n+ #if "bam" in $extension\n+ ln -s \'$myfiles.metadata.bam_index\' \'./read.${extension}.bai\' &&\n+ #end if\n $reads_temp.append("read." + str($extension))\n #end if\n \n NanoPlot\n --threads \\${GALAXY_SLOTS:-4}\n+ --tsv_stats\n --$mode.reads.type ${\' \'.join($reads_temp)}\n #if $filter.maxlength\n --maxlength $filter.maxlength\n@@ -46,15 +69,15 @@\n #if $filter.minqual\n --minqual $filter.minqual\n #end if\n+ #if $filter.runtime_until\n+ -- $filter.runtime_until\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@@ -63,8 +86,10 @@\n $filter.percentqual\n $filter.alength\n $filter.barcoded\n+ $filter.no_supplementary\n $customization.N50\n -o \'.\'\n+ && >&2 cat *log\n ]]></command>\n <inputs>\n <conditional name="mode">\n@@ -190,6 +215,11 @@\n optional="true"\n label="Drop reads with an average quality lower than specified."/>\n <param\n+ type="integer"\n+ argument="--runtime_until"\n+ optional="true"\n+ label="Only take the N first hours of a run"/>\n+ <param\n type="select"\n argument="--readtype"\n optional="true"\n@@ -204,6 +234,12 @@\n truevalue="--barcoded"\n falsevalue=""\n label="Use if you want to split the summary file by'..b' post filtering" />\n+ <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>\n+ <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>\n </outputs>\n <tests>\n <test>\n@@ -412,18 +430,30 @@\n <param name="choice" value="batch"/>\n <conditional name="reads">\n <param name="type" value="fastq_rich"/>\n- <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>\n+ <param name="files" value="reads.fastq.gz" ftype="fastqsanger.gz"/>\n </conditional>\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="plots" value="kde"/>\n </section>\n- <output name="output_html" file="NanoPlot-report.html" ftype="html" lines_diff="8" />\n- <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="txt"/>\n- <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>\n+ <output name="output_html" ftype="html">\n+ <assert_contents>\n+ <has_text text="html"/>\n+ <has_text text="mean_qual"/>\n+ </assert_contents>\n+ </output>\n+ <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>\n+ <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>\n+ <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size">\n+ </output>\n+ <output name="log_read_length" ftype="png">\n+ <assert_contents>\n+ <has_text text="PNG"/>\n+ </assert_contents>\n+ </output>\n </test>\n <test>\n <conditional name="mode">\n@@ -439,15 +469,18 @@\n </section>\n <section name="customization">\n <param name="color" value="yellow"/>\n- <param name="format" value="svg"/>\n </section>\n- <output name="output_html" file="bam-report.html" ftype="html" lines_diff="16">\n+ <output name="output_html" ftype="html">\n <assert_contents>\n <has_text text="html"/>\n <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->\n </assert_contents>\n </output>\n- <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>\n+ <output name="read_length" ftype="png">\n+ <assert_contents>\n+ <has_text text="PNG"/>\n+ </assert_contents>\n+ </output>\n </test>\n <test><!-- test with multiple input files -->\n <conditional name="mode">\n@@ -460,8 +493,8 @@\n <output name="output_html" ftype="html">\n <assert_contents>\n <has_text text="html"/>\n- <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->\n- <has_text text="<td>9.0</td>"/> <!--check both files were used 4+5 reads -->\n+ <not_has_text text="Aligned read length vs Percent identity plot using dots"/>\n+ <has_text text="<td>9</td>"/> <!--check both files were used 4+5 reads -->\n </assert_contents>\n </output>\n </test>\n' |
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| diff -r edbb6c5028f5 -r a3c4fe6f49ab test-data/HistogramReadlength.png |
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| Binary file test-data/HistogramReadlength.png has changed |
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| diff -r edbb6c5028f5 -r a3c4fe6f49ab test-data/NanoStats.txt --- a/test-data/NanoStats.txt Sun Jan 19 19:03:02 2020 -0500 +++ b/test-data/NanoStats.txt Thu Jun 16 20:08:15 2022 +0000 |
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| @@ -1,6 +1,25 @@ -General summary: -Mean read length: 2,564.9 -Median read length: 1,910.0 -Number of reads: 9.0 -Read length N50: 4,275.0 -Total bases: 23,084.0 +Metrics dataset +number_of_reads 371 +number_of_bases 8611871.0 +median_read_length 9390.0 +mean_read_length 23212.6 +read_length_stdev 42729.8 +n50 60395.0 +active_channels 169 +mean_qual 10.1 +median_qual 10.3 +longest_read_(with_Q):1 393431 (10.6) +longest_read_(with_Q):2 341725 (11.8) +longest_read_(with_Q):3 320662 (8.0) +longest_read_(with_Q):4 226843 (9.1) +longest_read_(with_Q):5 221901 (10.0) +highest_Q_read_(with_length):1 13.3 (6333) +highest_Q_read_(with_length):2 13.1 (5448) +highest_Q_read_(with_length):3 12.9 (27834) +highest_Q_read_(with_length):4 12.8 (20351) +highest_Q_read_(with_length):5 12.8 (97730) +Reads >Q5: 371 (100.0%) 8.6Mb +Reads >Q7: 371 (100.0%) 8.6Mb +Reads >Q10: 207 (55.8%) 4.7Mb +Reads >Q12: 49 (13.2%) 0.9Mb +Reads >Q15: 0 (0.0%) 0.0Mb |
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| diff -r edbb6c5028f5 -r a3c4fe6f49ab test-data/NanoStats_post_filtering.txt --- a/test-data/NanoStats_post_filtering.txt Sun Jan 19 19:03:02 2020 -0500 +++ b/test-data/NanoStats_post_filtering.txt Thu Jun 16 20:08:15 2022 +0000 |
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| @@ -1,27 +1,25 @@ -General summary: -Active channels: 169.0 -Mean read length: 23,212.6 -Mean read quality: 10.1 -Median read length: 9,390.0 -Median read quality: 10.3 -Number of reads: 371.0 -Read length N50: 60,395.0 -Total bases: 8,611,871.0 -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) +Metrics dataset +number_of_reads 371 +number_of_bases 8611871.0 +median_read_length 9390.0 +mean_read_length 23212.6 +read_length_stdev 42729.8 +n50 60395.0 +active_channels 169 +mean_qual 10.1 +median_qual 10.3 +longest_read_(with_Q):1 393431 (10.6) +longest_read_(with_Q):2 341725 (11.8) +longest_read_(with_Q):3 320662 (8.0) +longest_read_(with_Q):4 226843 (9.1) +longest_read_(with_Q):5 221901 (10.0) +highest_Q_read_(with_length):1 13.3 (6333) +highest_Q_read_(with_length):2 13.1 (5448) +highest_Q_read_(with_length):3 12.9 (27834) +highest_Q_read_(with_length):4 12.8 (20351) +highest_Q_read_(with_length):5 12.8 (97730) +Reads >Q5: 371 (100.0%) 8.6Mb +Reads >Q7: 371 (100.0%) 8.6Mb +Reads >Q10: 207 (55.8%) 4.7Mb +Reads >Q12: 49 (13.2%) 0.9Mb +Reads >Q15: 0 (0.0%) 0.0Mb |
