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Changeset 7:d59e7b82571d (2024-08-16)

Previous changeset 6:9d2730a2dc51 (2023-02-24) Next changeset 8:37a40027ae60 (2025-02-08)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 05ce3d2300557dd40f5faa8f25c2b26f00c7fdb2

modified:
nanoplot.xml
test-data/NanoStats.txt
test-data/NanoStats_post_filtering.txt

diff -r 9d2730a2dc51 -r d59e7b82571d nanoplot.xml
--- a/nanoplot.xml Fri Feb 24 08:38:39 2023 +0000
+++ b/nanoplot.xml Fri Aug 16 09:00:07 2024 +0000

[

b'@@ -1,61 +1,40 @@\n-<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="20.05">\n+<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="22.05">\n <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>\n <macros>\n- <token name="@TOOL_VERSION@">1.41.0</token>\n+ <token name="@TOOL_VERSION@">1.43.0</token>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">nanoplot</xref>\n+ </xrefs>\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+ \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+#set $myfiles = $mode.reads.files if $mode.choice == \'combined\' else [$mode.reads.files]\n #set reads_temp = []\n-#if $mode.choice == \'combined\':\n- #for $i, $f in enumerate($myfiles)\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.startswith("fastq"):\n- #set $extension = \'fastq\'\n+#for $i, $f in enumerate($myfiles)\n+ #if $f.ext.startswith("fastq"):\n+ #set $extension = "fastq" if "." not in $f.ext else "fastq.%s" % $f.ext.split(".")[-1]\n #else\n- #set $extension = $myfiles.ext\n- #end if\n- #if $myfiles.ext.endswith(".gz"):\n- #set $extension = $extension + ".gz"\n- #else if $myfiles.ext.endswith(".bz"):\n- #set $extension = $extension + "bz2"\n+ #set $extension = $f.ext\n #end if\n- ln -s \'$myfiles\' \'./read.$extension\' &&\n- #if "bam" in $extension\n- ln -s \'$myfiles.metadata.bam_index\' \'./read.${extension}.bai\' &&\n+ ln -s \'$f\' \'./read_${i}.$extension\' &&\n+ #if $extension == "bam"\n+ ln -s \'$f.metadata.bam_index\' \'./read_${i}.${extension}.bai\' &&\n #end if\n- $reads_temp.append("read." + str($extension))\n-#end if\n+ $reads_temp.append("read_" + str($i) + "." + str($extension))\n+#end for\n \n NanoPlot\n --threads \\${GALAXY_SLOTS:-4}\n --tsv_stats\n+ --no_static\n --$mode.reads.type ${\' \'.join($reads_temp)}\n #if $filter.maxlength\n --maxlength $filter.maxlength\n@@ -166,90 +145,26 @@\n </conditional>\n </when>\n </conditional>\n- <section\n- name="filter"\n- title="Options for filtering or transforming input prior to plotting"\n- expanded="false">\n- <param\n- type="integer"\n- argument="--maxlength"\n- optional="true"\n- label="Drop reads longer than length specified."/>\n- <param\n- type="integer"\n- argument="--minlength"\n- '..b'<data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>\n <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>\n- <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" />\n- <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${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 ${on_string}: Log Transformed Histogram Read Length"/>\n+ <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>\n+ \n+ \n </outputs>\n <tests>\n <test>\n@@ -447,13 +352,6 @@\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@@ -473,28 +371,26 @@\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"/> \n- </assert_contents>\n- </output>\n- <output name="read_length" ftype="png">\n- <assert_contents>\n- <has_text text="PNG"/>\n+ <has_text text="Aligned read length vs Percent identity plot using dots"/>\n+ \n </assert_contents>\n </output>\n </test>\n- <test>\n- <conditional name="mode">\n+ <test>\n+ \n+ <conditional name="mode">\n <param name="choice" value="combined"/>\n <conditional name="reads">\n <param name="type" value="fasta"/>\n- <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />\n+ <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta"/>\n </conditional>\n </conditional>\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"/>\n- <has_text text="<td>9</td>"/> \n+ <has_text text="<td>9</td>"/>\n+ \n </assert_contents>\n </output>\n </test>\n'

diff -r 9d2730a2dc51 -r d59e7b82571d test-data/NanoStats.txt
--- a/test-data/NanoStats.txt Fri Feb 24 08:38:39 2023 +0000
+++ b/test-data/NanoStats.txt Fri Aug 16 09:00:07 2024 +0000

@@ -6,7 +6,7 @@
read_length_stdev 42729.8
n50 60395.0
active_channels 169
-mean_qual 10.1
+mean_qual 9.3
median_qual 10.3
longest_read_(with_Q):1 393431 (10.6)
longest_read_(with_Q):2 341725 (11.8)
@@ -18,8 +18,8 @@
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
+Reads >Q20: 0 (0.0%) 0.0Mb
+Reads >Q25: 0 (0.0%) 0.0Mb
+Reads >Q30: 0 (0.0%) 0.0Mb

diff -r 9d2730a2dc51 -r d59e7b82571d test-data/NanoStats_post_filtering.txt
--- a/test-data/NanoStats_post_filtering.txt Fri Feb 24 08:38:39 2023 +0000
+++ b/test-data/NanoStats_post_filtering.txt Fri Aug 16 09:00:07 2024 +0000