Mercurial > repos > iuc > nanoplot
changeset 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 |
| files | nanoplot.xml test-data/NanoStats.txt test-data/NanoStats_post_filtering.txt |
| diffstat | 3 files changed, 43 insertions(+), 120 deletions(-) [+] |
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--- a/nanoplot.xml Fri Feb 24 08:38:52 2023 +0000 +++ b/nanoplot.xml Thu Mar 07 08:46:06 2024 +0000 @@ -1,14 +1,19 @@ -<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> - <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 @@ -56,6 +61,7 @@ NanoPlot --threads \${GALAXY_SLOTS:-4} --tsv_stats + --no_static --$mode.reads.type ${' '.join($reads_temp)} #if $filter.maxlength --maxlength $filter.maxlength @@ -166,90 +172,26 @@ </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 +341,20 @@ <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 +379,6 @@ </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 +398,26 @@ <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="<td>9</td>"/> <!--check both files were used 4+5 reads --> + <has_text text="<td>9</td>"/> + <!--check both files were used 4+5 reads --> </assert_contents> </output> </test>
--- a/test-data/NanoStats.txt Fri Feb 24 08:38:52 2023 +0000 +++ b/test-data/NanoStats.txt Thu Mar 07 08:46:06 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)
--- a/test-data/NanoStats_post_filtering.txt Fri Feb 24 08:38:52 2023 +0000 +++ b/test-data/NanoStats_post_filtering.txt Thu Mar 07 08:46:06 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)