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