# HG changeset patch
# User iuc
# Date 1723798807 0
# Node ID d59e7b82571d85408e28d684e7e938c3af5b767b
# Parent  9d2730a2dc51551d7d3bcb37b4587d23e06989d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 05ce3d2300557dd40f5faa8f25c2b26f00c7fdb2

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
@@ -1,61 +1,40 @@
-<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="20.05">
+<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="22.05">
     <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.41.0</token>
+        <token name="@TOOL_VERSION@">1.43.0</token>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">nanoplot</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
     </requirements>
-    <stdio>
-        <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />
-    </stdio>
+    <!--stdio>
+        Not needed anymore, because we do not generate the static PNGs anymore.
+        I will leave this in, in the case we activate the PNGs at some point again.
+        <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem"/>
+    </stdio-->
     <version_command>NanoPlot --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-## set TMPDIR if not already set by admin
-## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
-## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};
-
-#set $myfiles = $mode.reads.files
+#set $myfiles = $mode.reads.files if $mode.choice == 'combined' else [$mode.reads.files]
 #set reads_temp = []
-#if $mode.choice == 'combined':
-    #for $i, $f in enumerate($myfiles)
-        #if $f.ext.startswith("fastq"):
-            #set $extension = 'fastq'
-        #else
-            #set $extension = $f.ext
-        #end if
-        #if $f.ext.endswith(".gz"):
-            #set $f = $extension + ".gz"
-        #else if $f.ext.endswith(".bz"):
-            #set $extension = $extension + "bz2"
-        #end if
-        ln -s '$f' './read_${i}.$extension' &&
-        #if "bam" in $extension
-            ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' &&
-        #end if
-        $reads_temp.append("read_" + str($i) + "." + str($extension))
-    #end for
-#else
-    #if $myfiles.ext.startswith("fastq"):
-        #set $extension = 'fastq'
+#for $i, $f in enumerate($myfiles)
+    #if $f.ext.startswith("fastq"):
+       #set $extension = "fastq" if "." not in $f.ext else "fastq.%s" % $f.ext.split(".")[-1]
     #else
-        #set $extension = $myfiles.ext
-    #end if
-    #if $myfiles.ext.endswith(".gz"):
-        #set $extension = $extension + ".gz"
-    #else if $myfiles.ext.endswith(".bz"):
-        #set $extension = $extension + "bz2"
+        #set $extension = $f.ext
     #end if
-    ln -s '$myfiles' './read.$extension' &&
-    #if "bam" in $extension
-        ln -s '$myfiles.metadata.bam_index' './read.${extension}.bai' &&
+    ln -s '$f' './read_${i}.$extension' &&
+    #if $extension == "bam"
+        ln -s '$f.metadata.bam_index' './read_${i}.${extension}.bai' &&
     #end if
-    $reads_temp.append("read." + str($extension))
-#end if
+    $reads_temp.append("read_" + str($i) + "." + str($extension))
+#end for
 
 NanoPlot
     --threads \${GALAXY_SLOTS:-4}
     --tsv_stats
+    --no_static
     --$mode.reads.type ${' '.join($reads_temp)}
     #if $filter.maxlength
         --maxlength $filter.maxlength
@@ -166,90 +145,26 @@
                 </conditional>
             </when>
         </conditional>
-        <section
-            name="filter"
-            title="Options for filtering or transforming input prior to plotting"
-            expanded="false">
-            <param
-                type="integer"
-                argument="--maxlength"
-                optional="true"
-                label="Drop reads longer than length specified."/>
-            <param
-                type="integer"
-                argument="--minlength"
-                optional="true"
-                label="Drop reads shorter than length specified."/>
-            <param
-                type="boolean"
-                argument="--drop_outliers"
-                truevalue="--drop_outliers"
-                falsevalue=""
-                label="Drop outlier reads with extreme long length."/>
-            <param
-                type="integer"
-                argument="--downsample"
-                optional="true"
-                label="Reduce dataset to N reads by random sampling."/>
-            <param
-                type="boolean"
-                argument="--loglength"
-                truevalue="--loglength"
-                falsevalue=""
-                label="Logarithmic scaling of lengths in plots."/>
-            <param
-                type="boolean"
-                argument="--percentqual"
-                truevalue="--percentqual"
-                falsevalue=""
-                label="Use qualities as theoretical percent identities."/>
-            <param
-                type="boolean"
-                argument="--alength"
-                truevalue="--alength"
-                falsevalue=""
-                label="Use aligned read lengths rather than sequenced length (bam mode)."/>
-            <param
-                type="integer"
-                argument="--minqual"
-                optional="true"
-                label="Drop reads with an average quality lower than specified."/>
-            <param
-                type="integer"
-                argument="--runtime_until"
-                optional="true"
-                label="Only take the N first hours of a run"/>
-            <param
-                type="select"
-                argument="--readtype"
-                optional="true"
-                label="Which read type to extract information about from summary.">
+        <section name="filter" title="Options for filtering or transforming input prior to plotting" expanded="false">
+            <param argument="--maxlength" type="integer" optional="true" label="Drop reads longer than length specified."/>
+            <param argument="--minlength" type="integer" optional="true" label="Drop reads shorter than length specified."/>
+            <param argument="--drop_outliers" type="boolean" truevalue="--drop_outliers" falsevalue="" label="Drop outlier reads with extreme long length."/>
+            <param argument="--downsample" type="integer" optional="true" label="Reduce dataset to N reads by random sampling."/>
+            <param argument="--loglength" type="boolean" truevalue="--loglength" falsevalue="" label="Logarithmic scaling of lengths in plots."/>
+            <param argument="--percentqual" type="boolean" truevalue="--percentqual" falsevalue="" label="Use qualities as theoretical percent identities."/>
+            <param argument="--alength" type="boolean" truevalue="--alength" falsevalue="" label="Use aligned read lengths rather than sequenced length (bam mode)."/>
+            <param argument="--minqual" type="integer" optional="true" label="Drop reads with an average quality lower than specified."/>
+            <param argument="--runtime_until" type="integer" optional="true" label="Only take the N first hours of a run"/>
+            <param argument="--readtype" type="select" optional="true" label="Which read type to extract information about from summary.">
                 <option value="1D">1D</option>
                 <option value="2D">2D</option>
                 <option value="1D2">1D2</option>
             </param>
-            <param
-                type="boolean"
-                argument="--barcoded"
-                truevalue="--barcoded"
-                falsevalue=""
-                label="Use if you want to split the summary file by barcode."/>
-            <param
-                type="boolean"
-                argument="--no_supplementary"
-                truevalue="--no_supplementary"
-                falsevalue=""
-                label="Use if you want to remove supplementary alignments"/>
+            <param argument="--barcoded" type="boolean" truevalue="--barcoded" falsevalue="" label="Use if you want to split the summary file by barcode."/>
+            <param argument="--no_supplementary" type="boolean" truevalue="--no_supplementary" falsevalue="" label="Use if you want to remove supplementary alignments"/>
         </section>
-        <section
-            name="customization"
-            title="Options for customizing the plots created"
-            expanded="false">
-            <param
-                type="select"
-                argument="--color"
-                optional="true"
-                label="Specify a color for the plots.">
+        <section name="customization" title="Options for customizing the plots created" expanded="false">
+            <param type="select" argument="--color" optional="true" label="Specify a color for the plots.">
                 <option value="aliceblue">aliceblue</option>
                 <option value="antiquewhite">antiquewhite</option>
                 <option value="aqua">aqua</option>
@@ -399,30 +314,20 @@
                 <option value="yellowgreen">yellowgreen</option>
                 <option value="yellow">yellow</option>
             </param>
-            <param
-                type="select"
-                argument="--plots"
-                optional="true"
-                multiple="true"
-                display="checkboxes"
-                label="Specify the bivariate format of the plots.">
+            <param type="select" argument="--plots" optional="true" multiple="true" display="checkboxes" label="Specify the bivariate format of the plots.">
                 <option value="kde">kernel density estimation (kde)</option>
                 <option value="dot">dots (dot)</option>
             </param>
-            <param
-                type="boolean"
-                argument="--N50"
-                truevalue="--N50"
-                falsevalue=""
-                label="Show the N50 mark in the read length histogram."/>
+            <param type="boolean" argument="--N50" truevalue="--N50" falsevalue="" label="Show the N50 mark in the read length histogram."/>
         </section>
     </inputs>
     <outputs>
-        <data name="output_html" format="html" from_work_dir="NanoPlot-report.html"  label="${tool.name} on ${on_string}: HTML report"/>
+        <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
         <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
-        <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" />
-        <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
-        <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>
+        <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
+        <!-- https://github.com/wdecoster/NanoPlot/issues/352 generating PNGs can take much much longer to process. Not sure if this output is relevant at all -->
+        <!--data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
+        <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/-->
     </outputs>
     <tests>
         <test>
@@ -447,13 +352,6 @@
             </output>
             <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
             <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
-            <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size">
-            </output>
-            <output name="log_read_length" ftype="png">
-                <assert_contents>
-                    <has_text text="PNG"/>
-                </assert_contents>
-            </output>
         </test>
         <test>
             <conditional name="mode">
@@ -473,28 +371,26 @@
             <output name="output_html" ftype="html">
                 <assert_contents>
                     <has_text text="html"/>
-                    <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
-                </assert_contents>
-            </output>
-            <output name="read_length" ftype="png">
-                <assert_contents>
-                    <has_text text="PNG"/>
+                    <has_text text="Aligned read length vs Percent identity plot using dots"/>
+                    <!-- bam report specific -->
                 </assert_contents>
             </output>
         </test>
-        <test><!-- test with multiple input files -->
-             <conditional name="mode">
+        <test>
+            <!-- test with multiple input files -->
+            <conditional name="mode">
                 <param name="choice" value="combined"/>
                 <conditional name="reads">
                     <param name="type" value="fasta"/>
-                    <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
+                    <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta"/>
                 </conditional>
             </conditional>
             <output name="output_html" ftype="html">
                 <assert_contents>
                     <has_text text="html"/>
                     <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
-                    <has_text text="&lt;td&gt;9&lt;/td&gt;"/> <!--check both files were used 4+5 reads -->
+                    <has_text text="&lt;td&gt;9&lt;/td&gt;"/>
+                    <!--check both files were used 4+5 reads -->
                 </assert_contents>
             </output>
         </test>
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
@@ -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