Mercurial > repos > iuc > ggupset
diff ggupset.xml @ 0:889d574acce8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset commit 517bf38557204e91a3652046a9412fb635257c8f
| author | iuc |
|---|---|
| date | Sat, 17 Dec 2022 16:52:54 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ggupset.xml Sat Dec 17 16:52:54 2022 +0000 @@ -0,0 +1,54 @@ +<tool name="ggupset" id="emc-ggupset" version="1.0" profile="21.09"> + <description>produces plots of relationships, similar to venn diagrams.</description> + <requirements> + <requirement type="package" version="0.3.0">r-ggupset</requirement> + <requirement type="package" version="1.3.2">r-tidyverse</requirement> + </requirements> + <command><![CDATA[ +#for $f in $input + ln -s '$f' '$f.element_identifier'; +#end for + +Rscript '$__tool_directory__/upset.R' '$n_int' '$x_lab' '$y_lab' '$width' '$height' +#for $f in $input + '$f.element_identifier' +#end for +; +]]></command> + <inputs> + <param name="input" type="data" format="txt,tabular" multiple="true" label="Gene List files" /> + <param name="n_int" type="integer" min="1" max="100" value="40" label="Numer of interactions to show"/> + <param name="x_lab" type="text" value="Shared output across results" label="x-axis label"/> + <param name="y_lab" type="text" value="Number of shared results" label="y-axis label"/> + + <param name="width" type="integer" min="400" value="1000" label="Plot Width (px)"/> + <param name="height" type="integer" min="400" value="800" label="Plot Height (px)"/> + </inputs> + <outputs> + <data name="upset_freq" format="png" from_work_dir="upset-freq.png" label="${tool.name} on ${on_string}: Upset by frequency" /> + <data name="upset_degree" format="png" from_work_dir="upset-degree.png" label="${tool.name} on ${on_string}: Upset by degree" /> + <data name="commonalities" format="tabular" from_work_dir="upset.tsv" label="${tool.name} on ${on_string}: Identified Overlapping Groups" /> + </outputs> + <tests> + <test> + <param name="input" value="HEP3B,HUH,JHH6,JHH7,SNU"/> + <param name="n_int" value="40"/> + <param name="width" value="1000"/> + <param name="height" value="800"/> + <output name="upset_degree" ftype="png" compare="sim_size"> + <assert_contents> + <has_size value="82441" delta="10000" /> + </assert_contents> + </output> + <output name="upset_freq" ftype="png" compare="sim_size"> + <assert_contents> + <has_size value="81466" delta="10000" /> + </assert_contents> + </output> + <output name="commonalities" file="upset.tsv" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +`Upset plots <https://en.wikipedia.org/wiki/UpSet_Plot>`__ are a data visualisation similar to Venn diagrams, but extensible for many more than 3 sets. + ]]></help> +</tool>