Mercurial > repos > iuc > ampvis2_ordinate

comparison ordinate.xml @ 4:811df76f4f26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit ab75ba7665d7fb5c18ad08dfbba92b273f991dfc
author iuc
date Sat, 16 Mar 2024 11:32:14 +0000
parents 75e025c9bc10
children
comparison
equal deleted inserted replaced
3:75e025c9bc10 4:811df76f4f26
240 <tests> 240 <tests>
241 <!-- defaults (PCA) --> 241 <!-- defaults (PCA) -->
242 <test expect_num_outputs="2"> 242 <test expect_num_outputs="2">
243 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 243 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
244 <param name="output_screeplot" value="true"/> 244 <param name="output_screeplot" value="true"/>
245 <output name="plot" value="AalborgWWTPs-ordinate.pdf" ftype="pdf"/> 245 <output name="plot" value="AalborgWWTPs-ordinate.pdf" ftype="pdf" compare="sim_size"/>
246 <output name="screeplot" value="AalborgWWTPs-ordinate-screeplot.pdf" ftype="pdf"/> 246 <output name="screeplot" value="AalborgWWTPs-ordinate-screeplot.pdf" ftype="pdf" compare="sim_size"/>
247 </test> 247 </test>
248 <!-- RDA + caption --> 248 <!-- RDA + caption -->
249 <test expect_num_outputs="1"> 249 <test expect_num_outputs="1">
250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 250 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
251 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 251 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
253 <param name="type" value="RDA"/> 253 <param name="type" value="RDA"/>
254 <param name="distmeasure" value="manhattan"/> 254 <param name="distmeasure" value="manhattan"/>
255 <param name="transform" value="chi.square"/> 255 <param name="transform" value="chi.square"/>
256 <param name="constrain" value="Plant"/> 256 <param name="constrain" value="Plant"/>
257 </conditional> 257 </conditional>
258 <output name="plot" value="AalborgWWTPs-ordinate-rda.pdf" ftype="pdf"/> 258 <output name="plot" value="AalborgWWTPs-ordinate-rda.pdf" ftype="pdf" compare="sim_size"/>
259 </test> 259 </test>
260 <!-- MMDS + unfirac (which requires a tree) --> 260 <!-- MMDS + unfirac (which requires a tree) -->
261 <test expect_num_outputs="1"> 261 <test expect_num_outputs="1">
262 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/> 262 <param name="data" value="AalborgWWTPs-complete.rds" ftype="ampvis2"/>
263 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 263 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
264 <conditional name="type_cond"> 264 <conditional name="type_cond">
265 <param name="type" value="MMDS"/> 265 <param name="type" value="MMDS"/>
266 <param name="distmeasure" value="unifrac"/> 266 <param name="distmeasure" value="unifrac"/>
267 </conditional> 267 </conditional>
268 <output name="plot" value="AalborgWWTPs-ordinate-nmds.pdf" ftype="pdf"/> 268 <output name="plot" value="AalborgWWTPs-ordinate-nmds.pdf" ftype="pdf" compare="sim_size"/>
269 </test> 269 </test>
270 <!-- color, shape and colorframe --> 270 <!-- color, shape and colorframe -->
271 <test expect_num_outputs="1"> 271 <test expect_num_outputs="1">
272 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 272 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
273 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 273 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
274 <param name="sample_color_by" value="Year"/> 274 <param name="sample_color_by" value="Year"/>
275 <param name="sample_shape_by" value="Plant"/> 275 <param name="sample_shape_by" value="Plant"/>
276 <param name="sample_colorframe" value="Year"/> 276 <param name="sample_colorframe" value="Year"/>
277 <param name="sample_colorframe_label" value="Year"/> 277 <param name="sample_colorframe_label" value="Year"/>
278 <output name="plot" value="AalborgWWTPs-ordinate-color-shape-frame.pdf" ftype="pdf"/> 278 <output name="plot" value="AalborgWWTPs-ordinate-color-shape-frame.pdf" ftype="pdf" compare="sim_size"/>
279 </test> 279 </test>
280 <!-- label, trajectory --> 280 <!-- label, trajectory -->
281 <test expect_num_outputs="1"> 281 <test expect_num_outputs="1">
282 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 282 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
283 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 283 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
284 <param name="sample_label_by" value="Plant"/> 284 <param name="sample_label_by" value="Plant"/>
285 <param name="sample_trajectory" value="Year"/> 285 <param name="sample_trajectory" value="Year"/>
286 <output name="plot" value="AalborgWWTPs-ordinate-label-traj.pdf" ftype="pdf"/> 286 <output name="plot" value="AalborgWWTPs-ordinate-label-traj.pdf" ftype="pdf" compare="sim_size"/>
287 </test> 287 </test>
288 <!-- trajectory group --> 288 <!-- trajectory group -->
289 <test expect_num_outputs="1"> 289 <test expect_num_outputs="1">
290 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 290 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
291 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 291 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
292 <param name="sample_trajectory_group" value="Plant"/> 292 <param name="sample_trajectory_group" value="Plant"/>
293 <output name="plot" value="AalborgWWTPs-ordinate-label-traj-group.pdf" ftype="pdf"/> 293 <output name="plot" value="AalborgWWTPs-ordinate-label-traj-group.pdf" ftype="pdf" compare="sim_size"/>
294 </test> 294 </test>
295 <!-- species plot --> 295 <!-- species plot -->
296 <test expect_num_outputs="1"> 296 <test expect_num_outputs="1">
297 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 297 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
298 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 298 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
300 <param name="species_plot" value="TRUE"/> 300 <param name="species_plot" value="TRUE"/>
301 <param name="species_nlabels" value="2"/> 301 <param name="species_nlabels" value="2"/>
302 <param name="species_label_taxonomy" value="Family"/> 302 <param name="species_label_taxonomy" value="Family"/>
303 <param name="species_label_size" value="4"/> 303 <param name="species_label_size" value="4"/>
304 </conditional> 304 </conditional>
305 <output name="plot" value="AalborgWWTPs-ordinate-species.pdf" ftype="pdf"/> 305 <output name="plot" value="AalborgWWTPs-ordinate-species.pdf" ftype="pdf" compare="sim_size"/>
306 </test> 306 </test>
307 <!-- envfit factor--> 307 <!-- envfit factor-->
308 <test expect_num_outputs="1"> 308 <test expect_num_outputs="1">
309 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 309 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
310 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 310 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
311 <param name="envfit_factor" value="Plant"/> 311 <param name="envfit_factor" value="Plant"/>
312 <output name="plot" value="AalborgWWTPs-ordinate-envfit-factor.pdf" ftype="pdf"/> 312 <output name="plot" value="AalborgWWTPs-ordinate-envfit-factor.pdf" ftype="pdf" compare="sim_size"/>
313 </test> 313 </test>
314 <!-- envfit numeric--> 314 <!-- envfit numeric-->
315 <test expect_num_outputs="1"> 315 <test expect_num_outputs="1">
316 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 316 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
317 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 317 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
318 <param name="envfit_numeric" value="Year"/> 318 <param name="envfit_numeric" value="Year"/>
319 <output name="plot" value="AalborgWWTPs-ordinate-envfit-num.pdf" ftype="pdf"/> 319 <output name="plot" value="AalborgWWTPs-ordinate-envfit-num.pdf" ftype="pdf" compare="sim_size"/>
320 </test> 320 </test>
321 </tests> 321 </tests>
322 <help><![CDATA[ 322 <help><![CDATA[
323 What it does 323 What it does
324 ============ 324 ============