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planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
author iuc
date Wed, 26 Jun 2024 09:40:13 +0000
parents faacef62bb54
children
comparison
equal deleted inserted replaced
2:faacef62bb54 3:43ccbef89f1d
62 --random_effects \$random_effects 62 --random_effects \$random_effects
63 #end if 63 #end if
64 #if $fixed_effects 64 #if $fixed_effects
65 --fixed_effects \$fixed_effects 65 --fixed_effects \$fixed_effects
66 #end if 66 #end if
67 #if $reference
68 --reference '$reference'
69 #end if
70
67 #if $additional_options.correction 71 #if $additional_options.correction
68 --correction '$additional_options.correction' 72 --correction '$additional_options.correction'
69 #end if 73 #end if
70 $additional_options.standardize 74 $additional_options.standardize
71 $output.plot_heatmap 75 $output.plot_heatmap
72 #if $output.heatmap_first_n 76 #if $output.heatmap_first_n
73 --heatmap_first_n '$output.heatmap_first_n' 77 --heatmap_first_n '$output.heatmap_first_n'
74 #end if 78 #end if
75 $output.plot_scatter 79 $output.plot_scatter
76 --cores \${GALAXY_SLOTS:-4} 80 --cores 1
77 'input_data.tsv' 81 'input_data.tsv'
78 'input_metadata.tsv' 82 'input_metadata.tsv'
79 'outputFolder' 83 'outputFolder'
80 && 84 &&
81 cd outputFolder && mkdir -p figures/ && cp *.pdf figures 85 zip -r out.zip outputFolder &&
86 cd outputFolder &&
87 mkdir -p figures/ &&
88 cp *.pdf figures
89
82 90
83 ]]></command> 91 ]]></command>
84 <inputs> 92 <inputs>
85 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/> 93 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
86 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/> 94 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
87 <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " /> 95 <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
88
89 <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" /> 96 <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" />
90 97 <param argument="--reference" type="text" label="Reference" help="Reference for a variable with more than two levels provided as a string of 'variable,reference' comma delimited for multiple variables. " />
91
92
93 <section name="additional_options" title="Additional Options" expanded="true"> 98 <section name="additional_options" title="Additional Options" expanded="true">
94 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/> 99 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
95 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/> 100 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>
96 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/> 101 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/>
97 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply"> 102 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
112 <option value="CPLM">CPLM</option> 117 <option value="CPLM">CPLM</option>
113 <option value="NEGBIN">NEGBIN</option> 118 <option value="NEGBIN">NEGBIN</option>
114 <option value="ZINB">ZINB</option> 119 <option value="ZINB">ZINB</option>
115 </param> 120 </param>
116 <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH "> 121 <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH ">
117
118 <option value="BH">Benjamini-Hochberg(BH)</option> 122 <option value="BH">Benjamini-Hochberg(BH)</option>
119 <option value="BY">Benjamini-Yekutieli(BY)</option> 123 <option value="BY">Benjamini-Yekutieli(BY)</option>
120 </param> 124 <option value="Bonferroni">Bonferroni</option>
125 <option value="Holm">Holm</option>
126 <option value="Hochberg">Hochberg</option>
127 <option value="Hommel">Hommel</option>
128 </param>
121 <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/> 129 <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/>
122 </section> 130 </section>
123 <section name="output" title="Set Plotting Output" expanded="true"> 131 <section name="output" title="Set Plotting Output" expanded="true">
124 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/> 132 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/>
125 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/> 133 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/>
126 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/> 134 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/>
127 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/> 135 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/>
128 </section> 136 </section>
129 </inputs> 137 </inputs>
130 <outputs> 138 <outputs>
139 <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" />
131 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/> 140 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/>
132 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/> 141 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
133 <data name="residuals" format="rdata" from_work_dir="outputFolder/residuals.rds" label="Data frame with residuals for each feature"> 142 <data name="residuals" format="rdata" from_work_dir="outputFolder/fits/residuals.rds" label="Data frame with residuals for each feature">
134 <filter>output['residuals_output'] is True</filter> 143 <filter>output['residuals_output'] is True</filter>
135 </data> 144 </data>
136 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" > 145 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" >
137 <filter>output['plot_heatmap'] is True</filter> 146 <filter>output['plot_heatmap'] is True</filter>
138 </data> 147 </data>
140 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/> 149 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/>
141 <filter>output['plot_scatter'] is True</filter> 150 <filter>output['plot_scatter'] is True</filter>
142 </collection> 151 </collection>
143 </outputs> 152 </outputs>
144 <tests> 153 <tests>
145 <test expect_num_outputs="5"> 154 <test expect_num_outputs="6">
146 <param name="input_data" value="HMP2_taxonomy.tsv"/> 155 <param name="input_data" value="HMP2_taxonomy.tsv"/>
147 <param name="input_metadata" value="HMP2_metadata.tsv"/> 156 <param name="input_metadata" value="HMP2_metadata.tsv"/>
148 <param name="random_effects" value= "2,5"/> 157 <param name="random_effects" value= "2,5"/>
149 <param name="fixed_effects" value="4,9,10,11,6,3"/> 158 <param name="fixed_effects" value="4,9,10,11,6,3"/>
159 <param name="reference" value="diagnosis,nonIBD"/>
150 <section name="additional_options"> 160 <section name="additional_options">
151 <param name="min_abundance" value="0.0"/> 161 <param name="min_abundance" value="0.0"/>
152 <param name="min_prevalence" value="0.1"/> 162 <param name="min_prevalence" value="0.1"/>
153 <param name="max_significance" value="0.25"/> 163 <param name="max_significance" value="0.25"/>
154 <param name="normalization" value="NONE"/> 164 <param name="normalization" value="NONE"/>
161 <param name="plot_heatmap" value="true"/> 171 <param name="plot_heatmap" value="true"/>
162 <param name="heatmap_first_n" value="50"/> 172 <param name="heatmap_first_n" value="50"/>
163 <param name="plot_scatter" value="true"/> 173 <param name="plot_scatter" value="true"/>
164 <param name="residuals_output" value="true"/> 174 <param name="residuals_output" value="true"/>
165 </section> 175 </section>
176 <output name="archive_output">
177 <assert_contents>
178 <has_size value="15005328" delta="1000000" />
179 </assert_contents>
180 </output>
166 <output name="all_results"> 181 <output name="all_results">
167 <assert_contents> 182 <assert_contents>
168 <has_text text="feature"/> 183 <has_text text="feature"/>
169 <has_n_lines n="610"/> 184 <has_n_lines n="610"/>
170 <has_n_columns n="9"/> 185 <has_n_columns n="9"/>
171 </assert_contents> 186 </assert_contents>
172 </output> 187 </output>
173 <output name="significant_results"> 188 <output name="significant_results">
174 <assert_contents> 189 <assert_contents>
175 <has_text text="dysbiosisCD"/> 190 <has_text text="dysbiosisCD"/>
176 <has_n_lines n="159"/> 191 <has_n_lines n="159" delta="10"/>
177 <has_n_columns n="9"/> 192 <has_n_columns n="9"/>
178 </assert_contents> 193 </assert_contents>
179 </output> 194 </output>
180 <output name="residuals"> 195 <output name="residuals">
181 <assert_contents> 196 <assert_contents>
182 <has_size value="462746" delta="1000"/> 197 <has_size value="462386" />
183 </assert_contents> 198 </assert_contents>
184 </output> 199 </output>
185 <output name="headmap"> 200 <output name="headmap">
186 <assert_contents> 201 <assert_contents>
187 <has_size value="7373" delta="1000" /> 202 <has_size value="7373" delta="1000" />
223 <has_size value="1037005" delta="1000000" /> 238 <has_size value="1037005" delta="1000000" />
224 </assert_contents> 239 </assert_contents>
225 </element> 240 </element>
226 </output_collection> 241 </output_collection>
227 </test> 242 </test>
228 <test expect_num_outputs="5"> 243 <test expect_num_outputs="6">
229 <param name="input_data" value="HMP2_taxonomy.tsv"/> 244 <param name="input_data" value="HMP2_taxonomy.tsv"/>
230 <param name="input_metadata" value="HMP2_metadata.tsv"/> 245 <param name="input_metadata" value="HMP2_metadata.tsv"/>
231 <param name="fixed_effects" value="4,9"/> 246 <param name="fixed_effects" value="4,9"/>
247 <param name="reference" value="diagnosis,nonIBD"/>
232 <section name="additional_options"> 248 <section name="additional_options">
233 <param name="min_abundance" value="0.0"/> 249 <param name="min_abundance" value="0.0"/>
234 <param name="min_prevalence" value="0.1"/> 250 <param name="min_prevalence" value="0.1"/>
235 <param name="max_significance" value="0.25"/> 251 <param name="max_significance" value="0.25"/>
236 <param name="normalization" value="NONE"/> 252 <param name="normalization" value="NONE"/>
243 <param name="plot_heatmap" value="true"/> 259 <param name="plot_heatmap" value="true"/>
244 <param name="heatmap_first_n" value="50"/> 260 <param name="heatmap_first_n" value="50"/>
245 <param name="plot_scatter" value="true"/> 261 <param name="plot_scatter" value="true"/>
246 <param name="residuals_output" value="true"/> 262 <param name="residuals_output" value="true"/>
247 </section> 263 </section>
264 <output name="archive_output">
265 <assert_contents>
266 <has_size value="12630049" delta="1000000" />
267 </assert_contents>
268 </output>
248 <output name="all_results"> 269 <output name="all_results">
249 <assert_contents> 270 <assert_contents>
250 <has_text text="feature"/> 271 <has_text text="feature"/>
251 <has_n_lines n="262"/> 272 <has_n_lines n="262"/>
252 <has_n_columns n="9"/> 273 <has_n_columns n="9"/>
253 </assert_contents> 274 </assert_contents>
254 </output> 275 </output>
255 <output name="significant_results"> 276 <output name="significant_results">
256 <assert_contents> 277 <assert_contents>
257 <has_text text="diagnosis"/> 278 <has_text text="diagnosis"/>
258 <has_n_lines n="175"/> 279 <has_n_lines n="175" delta="5"/>
259 <has_n_columns n="9"/> 280 <has_n_columns n="9"/>
260 </assert_contents> 281 </assert_contents>
261 </output> 282 </output>
262 <output name="residuals"> 283 <output name="residuals">
263 <assert_contents> 284 <assert_contents>
264 <has_size value="367224" delta="1000"/> 285 <has_size value="366875"/>
265 </assert_contents> 286 </assert_contents>
266 </output> 287 </output>
267 <output_collection name="figures_pdfs" type="list"> 288 <output_collection name="figures_pdfs" type="list">
268 <element name="diagnosis.pdf" ftype="pdf"> 289 <element name="diagnosis.pdf" ftype="pdf">
269 <assert_contents> 290 <assert_contents>
270 <has_size value="6234127" delta="1000000" /> 291 <has_size value="6234127" delta="1000000" />
271 </assert_contents> 292 </assert_contents>
272 </element> 293 </element>
273 </output_collection> 294 </output_collection>
274 </test> 295 </test>
275 <test expect_num_outputs="5"> 296 <test expect_num_outputs="6">
276 <param name="input_data" value="HMP2_taxonomy.tsv"/> 297 <param name="input_data" value="HMP2_taxonomy.tsv"/>
277 <param name="input_metadata" value="HMP2_metadata.tsv"/> 298 <param name="input_metadata" value="HMP2_metadata.tsv"/>
278 <param name="fixed_effects" value="4,9"/> 299 <param name="fixed_effects" value="2,4"/>
300 <param name="reference" value="site,Cedars-Sinai,diagnosis,UC"/>
279 <section name="additional_options"> 301 <section name="additional_options">
280 <param name="min_abundance" value="0.0001"/> 302 <param name="min_abundance" value="0.0001"/>
281 <param name="min_prevalence" value="0.1"/> 303 <param name="min_prevalence" value="0.1"/>
282 <param name="max_significance" value="0.25"/> 304 <param name="max_significance" value="0.25"/>
283 <param name="normalization" value="NONE"/> 305 <param name="normalization" value="NONE"/>
290 <param name="plot_heatmap" value="true"/> 312 <param name="plot_heatmap" value="true"/>
291 <param name="heatmap_first_n" value="50"/> 313 <param name="heatmap_first_n" value="50"/>
292 <param name="plot_scatter" value="true"/> 314 <param name="plot_scatter" value="true"/>
293 <param name="residuals_output" value="true"/> 315 <param name="residuals_output" value="true"/>
294 </section> 316 </section>
317 <output name="archive_output">
318 <assert_contents>
319 <has_size value="18278259" delta="1000000" />
320 </assert_contents>
321 </output>
295 <output name="all_results"> 322 <output name="all_results">
296 <assert_contents> 323 <assert_contents>
297 <has_text text="feature"/> 324 <has_text text="feature"/>
298 <has_n_lines n="250"/> 325 <has_n_lines n="415" delta="10"/>
299 <has_n_columns n="9"/> 326 <has_n_columns n="9"/>
300 </assert_contents> 327 </assert_contents>
301 </output> 328 </output>
302 <output name="significant_results"> 329 <output name="significant_results">
303 <assert_contents> 330 <assert_contents>
304 <has_text text="diagnosis"/> 331 <has_text text="diagnosis"/>
305 <has_n_lines n="172"/> 332 <has_n_lines n="300" delta="15"/>
306 <has_n_columns n="9"/> 333 <has_n_columns n="9"/>
307 </assert_contents> 334 </assert_contents>
308 </output> 335 </output>
309 <output name="residuals"> 336 <output name="residuals">
310 <assert_contents> 337 <assert_contents>
311 <has_size value="359943" delta="1000"/> 338 <has_size value="363118"/>
312 </assert_contents> 339 </assert_contents>
313 </output> 340 </output>
314 <output name="headmap"> 341 <output name="headmap">
315 <assert_contents> 342 <assert_contents>
316 <has_size value="6554" delta="1000" /> 343 <has_size value="7000" delta="1000" />
317 </assert_contents> 344 </assert_contents>
318 </output> 345 </output>
319 <output_collection name="figures_pdfs" type="list"> 346 <output_collection name="figures_pdfs" type="list">
320 <element name="heatmap.pdf" ftype="pdf"> 347 <element name="heatmap.pdf" ftype="pdf">
321 <assert_contents> 348 <assert_contents>
322 <has_size value="6554" delta="1000" /> 349 <has_size value="7693" delta="100" />
323 </assert_contents> 350 </assert_contents>
324 </element> 351 </element>
325 <element name="diagnosis.pdf" ftype="pdf"> 352 <element name="diagnosis.pdf" ftype="pdf">
326 <assert_contents> 353 <assert_contents>
327 <has_size value="6061545" delta="1000000" /> 354 <has_size value="6061545" delta="1000000" />
328 </assert_contents> 355 </assert_contents>
329 </element> 356 </element>
330 <element name="dysbiosisnonIBD.pdf" ftype="pdf"> 357
331 <assert_contents>
332 <has_size value="2599373" delta="1000000" />
333 </assert_contents>
334 </element>
335 </output_collection> 358 </output_collection>
336 </test> 359 </test>
337 <test expect_num_outputs="5"> 360 <test expect_num_outputs="6">
338 <param name="input_data" value="HMP2_taxonomy.tsv"/> 361 <param name="input_data" value="HMP2_taxonomy.tsv"/>
339 <param name="input_metadata" value="HMP2_metadata.tsv"/> 362 <param name="input_metadata" value="HMP2_metadata.tsv"/>
363 <param name="fixed_effects" value="7,9"/>
340 <param name="random_effects" value="3" /> 364 <param name="random_effects" value="3" />
365
341 <section name="additional_options"> 366 <section name="additional_options">
342 <param name="min_abundance" value="0.0"/> 367 <param name="min_abundance" value="0.0"/>
343 <param name="min_prevalence" value="0.1"/> 368 <param name="min_prevalence" value="0.1"/>
344 <param name="max_significance" value="0.25"/> 369 <param name="max_significance" value="0.25"/>
345 <param name="normalization" value="TSS"/> 370 <param name="normalization" value="TSS"/>
352 <param name="plot_heatmap" value="true"/> 377 <param name="plot_heatmap" value="true"/>
353 <param name="heatmap_first_n" value="50"/> 378 <param name="heatmap_first_n" value="50"/>
354 <param name="plot_scatter" value="true"/> 379 <param name="plot_scatter" value="true"/>
355 <param name="residuals_output" value="true"/> 380 <param name="residuals_output" value="true"/>
356 </section> 381 </section>
382 <output name="archive_output">
383 <assert_contents>
384 <has_size value="8567935" delta="1000000" />
385 </assert_contents>
386 </output>
357 <output name="all_results"> 387 <output name="all_results">
358 <assert_contents> 388 <assert_contents>
359 <has_text text="feature"/> 389 <has_text text="feature"/>
360 <has_n_lines n="8092"/> 390 <has_n_lines n="175" delta="10"/>
361 <has_n_columns n="9"/> 391 <has_n_columns n="9"/>
362 </assert_contents> 392 </assert_contents>
363 </output> 393 </output>
364 <output name="significant_results"> 394 <output name="significant_results">
365 <assert_contents> 395 <assert_contents>
366 <has_text text="subject"/> 396 <has_text text="dysbiosisnonIBD"/>
367 <has_n_lines n="216" delta="5"/> 397 <has_n_lines n="95" delta="5"/>
368 <has_n_columns n="9"/> 398 <has_n_columns n="9"/>
369 </assert_contents> 399 </assert_contents>
370 </output> 400 </output>
371 <output name="residuals"> 401 <output name="residuals">
372 <assert_contents> 402 <assert_contents>
373 <has_size value="671142" delta="1000"/> 403 <has_size value="434087"/>
374 </assert_contents> 404 </assert_contents>
375 </output> 405 </output>
376 <output_collection name="figures_pdfs" type="list"> 406 <output_collection name="figures_pdfs" type="list">
377 <element name="heatmap.pdf" ftype="pdf"> 407 <element name="heatmap.pdf" ftype="pdf">
378 <assert_contents> 408 <assert_contents>
379 <has_size value="7000" delta="1000" /> 409 <has_size value="7000" delta="1000" />
380 </assert_contents> 410 </assert_contents>
381 </element> 411 </element>
382 </output_collection> 412 </output_collection>
383 </test> 413 </test>
384 <test expect_num_outputs="5"> 414
385 <param name="input_data" value="HMP2_taxonomy.tsv"/> 415
386 <param name="input_metadata" value="HMP2_metadata.tsv"/>
387
388 <section name="additional_options">
389 <param name="min_abundance" value="0.0"/>
390 <param name="min_prevalence" value="0.1"/>
391 <param name="max_significance" value="0.25"/>
392 <param name="normalization" value="TSS"/>
393 <param name="transform" value="LOG"/>
394 <param name="analysis_method" value="LM"/>
395 <param name="correction" value="BH"/>
396 <param name="standardize" value="True"/>
397 </section>
398 <section name="output">
399 <param name="plot_heatmap" value="true"/>
400 <param name="heatmap_first_n" value="50"/>
401 <param name="plot_scatter" value="true"/>
402 <param name="residuals_output" value="true"/>
403 </section>
404 <output name="all_results">
405 <assert_contents>
406 <has_text text="feature"/>
407 <has_n_lines n="8092"/>
408 <has_n_columns n="9"/>
409 </assert_contents>
410 </output>
411 <output name="significant_results">
412 <assert_contents>
413 <has_text text="subject"/>
414 <has_n_lines n="880"/>
415 <has_n_columns n="9"/>
416 </assert_contents>
417 </output>
418 <output name="residuals">
419 <assert_contents>
420 <has_size value="670759" delta="1000"/>
421 </assert_contents>
422 </output>
423 <output_collection name="figures_pdfs" type="list">
424 <element name="heatmap.pdf" ftype="pdf">
425 <assert_contents>
426 <has_size value="7900" delta="1000" />
427 </assert_contents>
428 </element>
429 </output_collection>
430 </test>
431 </tests> 416 </tests>
432 <help><![CDATA[ 417 <help><![CDATA[
433 @HELP_HEADER@ 418 @HELP_HEADER@
434 MaAsLin 2 419 MaAsLin 2
435 ========= 420 =========