Mercurial > repos > iuc > ggupset
comparison ggupset.xml @ 0:f005c350af7f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset commit 517bf38557204e91a3652046a9412fb635257c8f
author | iuc |
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date | Sat, 17 Dec 2022 16:53:08 +0000 |
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1 <tool name="ggupset" id="emc-ggupset" version="1.0" profile="21.09"> | |
2 <description>produces plots of relationships, similar to venn diagrams.</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.3.0">r-ggupset</requirement> | |
5 <requirement type="package" version="1.3.2">r-tidyverse</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 #for $f in $input | |
9 ln -s '$f' '$f.element_identifier'; | |
10 #end for | |
11 | |
12 Rscript '$__tool_directory__/upset.R' '$n_int' '$x_lab' '$y_lab' '$width' '$height' | |
13 #for $f in $input | |
14 '$f.element_identifier' | |
15 #end for | |
16 ; | |
17 ]]></command> | |
18 <inputs> | |
19 <param name="input" type="data" format="txt,tabular" multiple="true" label="Gene List files" /> | |
20 <param name="n_int" type="integer" min="1" max="100" value="40" label="Numer of interactions to show"/> | |
21 <param name="x_lab" type="text" value="Shared output across results" label="x-axis label"/> | |
22 <param name="y_lab" type="text" value="Number of shared results" label="y-axis label"/> | |
23 | |
24 <param name="width" type="integer" min="400" value="1000" label="Plot Width (px)"/> | |
25 <param name="height" type="integer" min="400" value="800" label="Plot Height (px)"/> | |
26 </inputs> | |
27 <outputs> | |
28 <data name="upset_freq" format="png" from_work_dir="upset-freq.png" label="${tool.name} on ${on_string}: Upset by frequency" /> | |
29 <data name="upset_degree" format="png" from_work_dir="upset-degree.png" label="${tool.name} on ${on_string}: Upset by degree" /> | |
30 <data name="commonalities" format="tabular" from_work_dir="upset.tsv" label="${tool.name} on ${on_string}: Identified Overlapping Groups" /> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="input" value="HEP3B,HUH,JHH6,JHH7,SNU"/> | |
35 <param name="n_int" value="40"/> | |
36 <param name="width" value="1000"/> | |
37 <param name="height" value="800"/> | |
38 <output name="upset_degree" ftype="png" compare="sim_size"> | |
39 <assert_contents> | |
40 <has_size value="82441" delta="10000" /> | |
41 </assert_contents> | |
42 </output> | |
43 <output name="upset_freq" ftype="png" compare="sim_size"> | |
44 <assert_contents> | |
45 <has_size value="81466" delta="10000" /> | |
46 </assert_contents> | |
47 </output> | |
48 <output name="commonalities" file="upset.tsv" ftype="tabular"/> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 `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. | |
53 ]]></help> | |
54 </tool> |