nanoplot: nanoplot.xml comparison

comparison nanoplot.xml @ 7:7b379e98b9a9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab

author	iuc
date	Thu, 07 Mar 2024 08:46:06 +0000
parents	0f1c34698076
children	a02b8b3f5a0c

comparison

equal deleted inserted replaced

-:0f1c34698076
+:7b379e98b9a9
-<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@">1.42.0</token>
 </macros>
+<xrefs>
+<xref type="bio.tools">nanoplot</xref>
+</xrefs>
 <requirements>
 <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
 </requirements>
-<stdio>
+<!--stdio>
-<regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />
+Not needed anymore, because we do not generate the static PNGs anymore.
-</stdio>
+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};
 #end if
 NanoPlot
 --threads \${GALAXY_SLOTS:-4}
 --tsv_stats
+--no_static
 --$mode.reads.type ${' '.join($reads_temp)}
 #if $filter.maxlength
 --maxlength $filter.maxlength
 #end if
 #if $filter.minlength
 <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
 </when>
 </conditional>
 </when>
 </conditional>
-<section
+<section name="filter" title="Options for filtering or transforming input prior to plotting" expanded="false">
-name="filter"
+<param argument="--maxlength" type="integer" optional="true" label="Drop reads longer than length specified."/>
-title="Options for filtering or transforming input prior to plotting"
+<param argument="--minlength" type="integer" optional="true" label="Drop reads shorter than length specified."/>
-expanded="false">
+<param argument="--drop_outliers" type="boolean" truevalue="--drop_outliers" falsevalue="" label="Drop outlier reads with extreme long length."/>
-<param
+<param argument="--downsample" type="integer" optional="true" label="Reduce dataset to N reads by random sampling."/>
-type="integer"
+<param argument="--loglength" type="boolean" truevalue="--loglength" falsevalue="" label="Logarithmic scaling of lengths in plots."/>
-argument="--maxlength"
+<param argument="--percentqual" type="boolean" truevalue="--percentqual" falsevalue="" label="Use qualities as theoretical percent identities."/>
-optional="true"
+<param argument="--alength" type="boolean" truevalue="--alength" falsevalue="" label="Use aligned read lengths rather than sequenced length (bam mode)."/>
-label="Drop reads longer than length specified."/>
+<param argument="--minqual" type="integer" optional="true" label="Drop reads with an average quality lower than specified."/>
-<param
+<param argument="--runtime_until" type="integer" optional="true" label="Only take the N first hours of a run"/>
-type="integer"
+<param argument="--readtype" type="select" optional="true" label="Which read type to extract information about from summary.">
-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.">
 <option value="1D">1D</option>
 <option value="2D">2D</option>
 <option value="1D2">1D2</option>
 </param>
-<param
+<param argument="--barcoded" type="boolean" truevalue="--barcoded" falsevalue="" label="Use if you want to split the summary file by barcode."/>
-type="boolean"
+<param argument="--no_supplementary" type="boolean" truevalue="--no_supplementary" falsevalue="" label="Use if you want to remove supplementary alignments"/>
-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"/>
 </section>
-<section
+<section name="customization" title="Options for customizing the plots created" expanded="false">
-name="customization"
+<param type="select" argument="--color" optional="true" label="Specify a color for the plots.">
-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>
 <option value="aquamarine">aquamarine</option>
 <option value="azure">azure</option>
 <option value="whitesmoke">whitesmoke</option>
 <option value="white">white</option>
 <option value="yellowgreen">yellowgreen</option>
 <option value="yellow">yellow</option>
 </param>
-<param
+<param type="select" argument="--plots" optional="true" multiple="true" display="checkboxes" label="Specify the bivariate format of the plots.">
-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
+<param type="boolean" argument="--N50" truevalue="--N50" falsevalue="" label="Show the N50 mark in the read length histogram."/>
-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 ${on_string}: NanoStats post filtering" />
+<data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
-<data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
+<!-- https://github.com/wdecoster/NanoPlot/issues/352 generating PNGs can take much much longer to process. Not sure if this output is relevant at all -->
-<data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>
+<!--data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${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>
 <conditional name="mode">
 <param name="choice" value="batch"/>
 <has_text text="mean_qual"/>
 </assert_contents>
 </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">
 <param name="choice" value="combined"/>
 <conditional name="reads">
 <param name="color" value="yellow"/>
 </section>
 <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 -->
+<has_text text="Aligned read length vs Percent identity plot using dots"/>
-</assert_contents>
+<!-- bam report specific -->
-</output>
-<output name="read_length" ftype="png">
-<assert_contents>
-<has_text text="PNG"/>
 </assert_contents>
 </output>
 </test>
-<test><!-- test with multiple input files -->
+<test>
-<conditional name="mode">
+<!-- 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>
 </tests>
 <help>

Mercurial > repos > iuc > nanoplot

comparison nanoplot.xml @ 7:7b379e98b9a9 draft