| Previous changeset 6:0f1c34698076 (2023-02-24) Next changeset 8:a02b8b3f5a0c (2024-04-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab |
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modified:
nanoplot.xml test-data/NanoStats.txt test-data/NanoStats_post_filtering.txt |
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| diff -r 0f1c34698076 -r 7b379e98b9a9 nanoplot.xml --- a/nanoplot.xml Fri Feb 24 08:38:52 2023 +0000 +++ b/nanoplot.xml Thu Mar 07 08:46:06 2024 +0000 |
| [ |
| b'@@ -1,14 +1,19 @@\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@">1.42.0</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+ <!--stdio>\n+ Not needed anymore, because we do not generate the static PNGs anymore.\n+ I will leave this in, in the case we activate the PNGs at some point again.\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@@ -56,6 +61,7 @@\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 $filter.maxlength\n@@ -166,90 +172,26 @@\n </conditional>\n </when>\n </conditional>\n- <section\n- name="filter"\n- title="Options for filtering or transforming input prior to plotting"\n- expanded="false">\n- <param\n- type="integer"\n- argument="--maxlength"\n- optional="true"\n- label="Drop reads longer than length specified."/>\n- <param\n- type="integer"\n- argument="--minlength"\n- optional="true"\n- label="Drop reads shorter than length specified."/>\n- <param\n- type="boolean"\n- argument="--drop_outliers"\n- truevalue="--drop_outliers"\n- falsevalue=""\n- label="Drop outlier reads with extreme long length."/>\n- <param\n- type="integer"\n- argument="--downsample"\n- optional="true"\n- label="Reduce dataset to N reads by random sampling."/>\n- <param\n- type="boolean"\n- argument="--loglength"\n- truevalue="--loglength"\n- falsevalue=""\n- label="Logarithmic scaling of lengths in plots."/>\n- <param\n- type="boolean"\n- argument="--percentqual"\n- truevalue="--percentqual"\n- falsevalue=""\n- label="Use qualities as theoretical percent identities."/>\n- <param\n- type="boolean"\n- argument="--alength"\n- truevalue="--alength"\n- falsevalue=""\n- label="Use aligned read lengths rather than sequenced length (bam mode)."/>\n- <param\n- type="integer"\n- argument="--minqual"\n- optional="true"\n- label="Drop reads with an average quality lower than specified."/>\n- <param\n- type="integer"\n- argument="--runtime_until"\n- optional="true"\n- label="Only take the N first hours of a run"/>\n- <param\n- type="select"\n- argument="--readtype"\n- optional="true"\n- label="Which read type to extract information about from summary.">\n+ <section name="filter" title="Options for filtering or transforming i'..b'<data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${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 ${on_string}: NanoStats post filtering"/>\n+ <!-- https://github.com/wdecoster/NanoPlot/issues/352 generating PNGs can take much much longer to process. Not sure if this output is relevant at all -->\n+ <!--data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${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@@ -447,13 +379,6 @@\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 +398,26 @@\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"/> <!-- bam report specific -->\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+ <!-- bam report specific -->\n </assert_contents>\n </output>\n </test>\n- <test><!-- test with multiple input files -->\n- <conditional name="mode">\n+ <test>\n+ <!-- test with multiple input files -->\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>"/> <!--check both files were used 4+5 reads -->\n+ <has_text text="<td>9</td>"/>\n+ <!--check both files were used 4+5 reads -->\n </assert_contents>\n </output>\n </test>\n' |
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| diff -r 0f1c34698076 -r 7b379e98b9a9 test-data/NanoStats.txt --- 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 |
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| @@ -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) |
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| diff -r 0f1c34698076 -r 7b379e98b9a9 test-data/NanoStats_post_filtering.txt --- 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 |
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| @@ -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) |