view ggupset.xml @ 0:f005c350af7f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset commit 517bf38557204e91a3652046a9412fb635257c8f

<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>