Mercurial > repos > iuc > ampvis2_heatmap
comparison heatmap.xml @ 4:14695ae019be draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit ab75ba7665d7fb5c18ad08dfbba92b273f991dfc
| author | iuc |
|---|---|
| date | Sat, 16 Mar 2024 11:31:43 +0000 |
| parents | a2d4da20749a |
| children |
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| 3:a2d4da20749a | 4:14695ae019be |
|---|---|
| 198 </outputs> | 198 </outputs> |
| 199 <tests> | 199 <tests> |
| 200 <!-- defaults --> | 200 <!-- defaults --> |
| 201 <test expect_num_outputs="1"> | 201 <test expect_num_outputs="1"> |
| 202 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 202 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 203 <output name="plot" value="AalborgWWTPs-heatmap.pdf" ftype="pdf"/> | 203 <output name="plot" value="AalborgWWTPs-heatmap.pdf" ftype="pdf" compare="sim_size"/> |
| 204 </test> | 204 </test> |
| 205 <!-- group and facet--> | 205 <!-- group and facet--> |
| 206 <test expect_num_outputs="1"> | 206 <test expect_num_outputs="1"> |
| 207 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 207 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 208 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | 208 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> |
| 209 <param name="group_by" value="Plant"/> | 209 <param name="group_by" value="Plant"/> |
| 210 <param name="facet_by" value="Year"/> | 210 <param name="facet_by" value="Year"/> |
| 211 <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.pdf" ftype="pdf"/> | 211 <output name="plot_raw" value="AalborgWWTPs-heatmap-group-facet.pdf" ftype="pdf" compare="sim_size"/> |
| 212 </test> | 212 </test> |
| 213 <!-- group and facet and test raw output --> | 213 <!-- group and facet and test raw output --> |
| 214 <test expect_num_outputs="1"> | 214 <test expect_num_outputs="1"> |
| 215 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 215 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 216 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | 216 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> |
| 221 </test> | 221 </test> |
| 222 <!-- normalise --> | 222 <!-- normalise --> |
| 223 <test expect_num_outputs="1"> | 223 <test expect_num_outputs="1"> |
| 224 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 224 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 225 <param name="normalise" value="true"/> | 225 <param name="normalise" value="true"/> |
| 226 <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf"/> | 226 <output name="plot" value="AalborgWWTPs-heatmap-normalise.pdf" ftype="pdf" compare="sim_size"/> |
| 227 </test> | 227 </test> |
| 228 <!-- normalise by a specific sample --> | 228 <!-- normalise by a specific sample --> |
| 229 <test expect_num_outputs="1"> | 229 <test expect_num_outputs="1"> |
| 230 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 230 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 231 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | 231 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> |
| 232 <param name="normalise" value="true"/> | 232 <param name="normalise" value="true"/> |
| 233 <param name="normalise_by" value="16SAMP-747"/> | 233 <param name="normalise_by" value="16SAMP-747"/> |
| 234 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf"/> | 234 <output name="plot" value="AalborgWWTPs-heatmap-normalise_by_sample.pdf" ftype="pdf" compare="sim_size"/> |
| 235 </test> | 235 </test> |
| 236 <!-- normalise by a metadata variable | 236 <!-- normalise by a metadata variable |
| 237 https://github.com/KasperSkytte/ampvis2/issues/168 --> | 237 https://github.com/KasperSkytte/ampvis2/issues/168 --> |
| 238 <!-- <test expect_num_outputs="1"> | 238 <!-- <test expect_num_outputs="1"> |
| 239 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 239 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 251 <param name="tax_aggregate" value="Order"/> | 251 <param name="tax_aggregate" value="Order"/> |
| 252 <param name="tax_add" value="Class"/> | 252 <param name="tax_add" value="Class"/> |
| 253 <param name="tax_show" value="5"/> | 253 <param name="tax_show" value="5"/> |
| 254 <param name="showRemainingTaxa" value="true"/> | 254 <param name="showRemainingTaxa" value="true"/> |
| 255 <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf"/> | 255 <output name="plot" value="AalborgWWTPs-heatmap-tax.pdf" ftype="pdf" compare="sim_size"/> |
| 256 </test> | 256 </test> |
| 257 <!-- sort by a specific sample --> | 257 <!-- sort by a specific sample --> |
| 258 <test expect_num_outputs="1"> | 258 <test expect_num_outputs="1"> |
| 259 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 259 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 260 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | 260 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> |
| 261 <conditional name="sort_by_cond"> | 261 <conditional name="sort_by_cond"> |
| 262 <param name="sort_by_sel" value="sample"/> | 262 <param name="sort_by_sel" value="sample"/> |
| 263 <param name="sort_by" value="16SAMP-747"/> | 263 <param name="sort_by" value="16SAMP-747"/> |
| 264 </conditional> | 264 </conditional> |
| 265 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_sample.pdf" ftype="pdf"/> | 265 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_sample.pdf" ftype="pdf" compare="sim_size"/> |
| 266 </test> | 266 </test> |
| 267 <!-- sort by a group of samples --> | 267 <!-- sort by a group of samples --> |
| 268 <test expect_num_outputs="1"> | 268 <test expect_num_outputs="1"> |
| 269 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 269 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 270 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> | 270 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> |
| 271 <param name="group_by" value="Period"/> | 271 <param name="group_by" value="Period"/> |
| 272 <conditional name="sort_by_cond"> | 272 <conditional name="sort_by_cond"> |
| 273 <param name="sort_by_sel" value="group"/> | 273 <param name="sort_by_sel" value="group"/> |
| 274 <param name="sort_by" value="Winter"/> | 274 <param name="sort_by" value="Winter"/> |
| 275 </conditional> | 275 </conditional> |
| 276 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_group.pdf" ftype="pdf"/> | 276 <output name="plot" value="AalborgWWTPs-heatmap-sort_by_group.pdf" ftype="pdf" compare="sim_size"/> |
| 277 </test> | 277 </test> |
| 278 <test expect_num_outputs="1"> | 278 <test expect_num_outputs="1"> |
| 279 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 279 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 280 <param name="tax_aggregate" value="Genus"/> | 280 <param name="tax_aggregate" value="Genus"/> |
| 281 <conditional name="plot_functions_cond"> | 281 <conditional name="plot_functions_cond"> |
| 282 <param name="plot_functions_sel" value="midasfieldguide"/> | 282 <param name="plot_functions_sel" value="midasfieldguide"/> |
| 283 <param name="functions" value="MiDAS,Filamentous,AOB,NOB,GAO"/> | 283 <param name="functions" value="MiDAS,Filamentous,AOB,NOB,GAO"/> |
| 284 </conditional> | 284 </conditional> |
| 285 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_midas.pdf" ftype="pdf"/> | 285 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_midas.pdf" ftype="pdf" compare="sim_size"/> |
| 286 </test> | 286 </test> |
| 287 <test expect_num_outputs="1"> | 287 <test expect_num_outputs="1"> |
| 288 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> | 288 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> |
| 289 <param name="tax_aggregate" value="Genus"/> | 289 <param name="tax_aggregate" value="Genus"/> |
| 290 <conditional name="plot_functions_cond"> | 290 <conditional name="plot_functions_cond"> |
| 291 <param name="plot_functions_sel" value="file"/> | 291 <param name="plot_functions_sel" value="file"/> |
| 292 <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/> | 292 <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/> |
| 293 <param name="functions" value="Foo,Bar"/> | 293 <param name="functions" value="Foo,Bar"/> |
| 294 </conditional> | 294 </conditional> |
| 295 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf"/> | 295 <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/> |
| 296 </test> | 296 </test> |
| 297 | 297 |
| 298 </tests> | 298 </tests> |
| 299 <help><![CDATA[ | 299 <help><![CDATA[ |
| 300 What it does | 300 What it does |