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fix isoplot with R function from graphstatsr r package#393

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erifa1 wants to merge 5 commits intoworkflow4metabolomics:masterfrom
erifa1:fix_isoplot
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fix isoplot with R function from graphstatsr r package#393
erifa1 wants to merge 5 commits intoworkflow4metabolomics:masterfrom
erifa1:fix_isoplot

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@erifa1 erifa1 commented Jan 16, 2026

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

Fix IsoPlot tool: First version of Isoplot (https://github.com/llegregam/Isoplot) has been developed in 2021. This new version of Isoplot is now integrated in the R package GraphStatsR (https://forge.inrae.fr/etienne.rifa/graphstats). It has been re-written using the R Shiny framework to provide a more user-friendly interface and new functionalities.

Tests pass with planemo.

lecorguille
lecorguille requested changes Jan 20, 2026
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tools/isoplot/isoplot.xml Outdated
}</citation>
</citations>
</tool>
<tool id="isoplot" name="IsoPlot" version="0.1">
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@lecorguille lecorguille Jan 20, 2026

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The version number should be something linked to graphstatsr, isn't it?
At least > 1.3.1, that correspond the last isoplot version.

Can you also add a profile?

tools/isoplot/isoplot.xml Outdated
</stdio>

<command><![CDATA[
Rscript -e "library(graphstatsr); print('Running GraphstatsR'); graphstatsr::IsoPlot_fun(feat_table = '$feat_tab', metadata_table = '$meta_tab', groups = '$groups', relativeCID = '$relative_cid', dodgeCID = '$dodge_cid', outpath = './isoplot_results', pdf = TRUE, img = TRUE); print('OK'); print(getwd()); tar('isoplot_results.tgz', list.files('./isoplot_results', full.names = TRUE), compression = 'gzip'); print(dir());print(file.exists('isoplot_results.tgz'))"
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@lecorguille lecorguille Jan 20, 2026

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Can you write the command on multilines?
Galaxy will remove the carriage return "\n".

tools/isoplot/isoplot.xml Outdated
</inputs>

<outputs>
<data name="out_tgz" label="isoplot_results.tgz" format="tgz" from_work_dir="isoplot_results.tgz"/>
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@lecorguille lecorguille Jan 20, 2026

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You should use a variable instead of isoplot_results.tgz(and so in the command template)

tools/isoplot/isoplot.xml Outdated
]]></command>

<inputs>
<param name='feat_tab' type='data' format='tabular' label='Upload feature table data that has been corrected by Isocor (tabular/tsv format)' />
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@lecorguille lecorguille Jan 20, 2026

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Remove Upload.
We can't guess if this file could be generate at some point by another tool?

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@erifa1 erifa1 Jan 20, 2026

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Information added in documentation

tools/isoplot/isoplot.xml Outdated
Comment on lines +49 to +55
<!-- <outputs>
<data name="out_tgz" from_work_dir="isoplot_results.tgz">
<assert_contents>
<has_size value="1000000" delta="5000"/>
</assert_contents>
</data>
</outputs> -->
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@lecorguille lecorguille Jan 20, 2026

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Remove this or at least move it in the corresponding test element

tools/isoplot/isoplot.xml
</outputs> -->


<help><![CDATA[
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@lecorguille lecorguille Jan 20, 2026

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It's really look like a complet new tool compare to the former one.

Could be interesting to add a line about that and the retro-compabilitility?

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@erifa1 erifa1 Jan 20, 2026

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As the tool has been completely rewritten in R using a Shiny-oriented approach, a command-line interface was adapted to provide equivalent functionality. However, backward compatibility with the previous version of isoplot cannot be guaranteed.

tools/isoplot/.shed.yml Outdated
@@ -1,8 +1,8 @@
name: isoplot
name: graphstatsr::isoplot
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@lecorguille lecorguille Jan 20, 2026

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If you change the repo name, you will have maybe to depricate the former one?

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@erifa1 erifa1 Jan 20, 2026

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We can preserve the name isoplot, as the tool only uses the isoplot function from the graphstatsr package.

tools/isoplot/isoplot.xml Outdated
</inputs>

<outputs>
<data name="out_tgz" label="isoplot_results.tgz" format="tgz" from_work_dir="isoplot_results.tgz"/>
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@lecorguille lecorguille Jan 20, 2026

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.tgz is a dead end that can't be use in downstream steps.

That contains the archive?

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@erifa1 erifa1 Jan 20, 2026

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Correct, the .tgz file is an archive of the results, and no downstream processing is expected after this step.

tools/isoplot/isoplot.xml Outdated
</inputs>

<outputs>
<data name="out_tgz" label="isoplot_results.tgz" format="tgz" from_work_dir="isoplot_results.tgz"/>
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@lecorguille lecorguille Jan 20, 2026

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Can you change the label for something more explicite and informative?

tools/isoplot/isoplot.xml
Comment on lines +85 to +86
feat_table Feature table corrected by IsoCor (CSV or TSV format)
metadata Metadata table describing samples and experimental groups
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@lecorguille lecorguille Jan 20, 2026

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Do you have somewhere a documentation on how to generate those tabular file with the mandatory columns... ?

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erifa1 commented Jan 20, 2026

@lecorguille Thanks for the review, please let me know if any further changes are needed.

@erifa1 erifa1 requested a review from lecorguille February 25, 2026 08:14
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@erifa1 @lecorguille