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planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
author iuc
date Mon, 29 Apr 2024 10:33:48 +0000
parents ef2cace85809
children
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1:ef2cace85809 2:faacef62bb54
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="xrefs"/> 7 <expand macro="xrefs"/>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10
11 ## get column names of fixed and random effect from the input file, since galaxy
12 ## can only return indices with type="data_column"
13 ## using awk so that the file is only parsed on command line execution
14
15 #if $fixed_effects
16 #set idx = []
17 #for $i in $fixed_effects:
18 #silent idx.append(f'${i}')
19 #end for
20 #set idx_for_awk = ','.join(idx)
21
22 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
23 echo 'Assigned fixed effects as:' \$fixed_effects &&
24 #end if
25
26
27 #if $random_effects
28 #set idx = []
29 #for $i in $random_effects:
30 #silent idx.append(f'${i}')
31 #end for
32 #set idx_for_awk = ','.join(idx)
33
34 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
35 echo 'Assigned random effects as:' \$random_effects &&
36 #end if
37
10 ln -s '$input_data' 'input_data.tsv' 38 ln -s '$input_data' 'input_data.tsv'
11 && 39 &&
12 ln -s '$input_metadata' 'input_metadata.tsv' 40 ln -s '$input_metadata' 'input_metadata.tsv'
13 && 41 &&
14 Maaslin2.R 42 Maaslin2.R
29 #end if 57 #end if
30 #if $additional_options.analysis_method 58 #if $additional_options.analysis_method
31 --analysis_method '$additional_options.analysis_method' 59 --analysis_method '$additional_options.analysis_method'
32 #end if 60 #end if
33 #if $random_effects 61 #if $random_effects
34 --random_effects '$random_effects' 62 --random_effects \$random_effects
35 #end if 63 #end if
36 #if $fixed_effects 64 #if $fixed_effects
37 --fixed_effects '$fixed_effects' 65 --fixed_effects \$fixed_effects
38 #end if 66 #end if
39 #if $additional_options.correction 67 #if $additional_options.correction
40 --correction '$additional_options.correction' 68 --correction '$additional_options.correction'
41 #end if 69 #end if
42 $additional_options.standardize 70 $additional_options.standardize
49 'input_data.tsv' 77 'input_data.tsv'
50 'input_metadata.tsv' 78 'input_metadata.tsv'
51 'outputFolder' 79 'outputFolder'
52 && 80 &&
53 cd outputFolder && mkdir -p figures/ && cp *.pdf figures 81 cd outputFolder && mkdir -p figures/ && cp *.pdf figures
82
54 ]]></command> 83 ]]></command>
55 <inputs> 84 <inputs>
56 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/> 85 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
57 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/> 86 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
58 <param argument="--fixed_effects" type="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects"> 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 " />
59 <option value="diagnosis" selected="true">diagnosis</option> 88
60 <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option> 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" />
61 <option value="dysbiosisUC" selected="true">dysbiosisUC</option> 90
62 <option value="dysbiosisCD" selected="true">dysbiosisCD</option> 91
63 <option value="antibiotics" selected="true">antibiotics</option> 92
64 <option value="age" selected="true">age</option>
65 </param>
66 <param argument="--random_effects" type="text" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects"/>
67 <section name="additional_options" title="Additional Options" expanded="true"> 93 <section name="additional_options" title="Additional Options" expanded="true">
68 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/> 94 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
69 <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"/> 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"/>
70 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/> 96 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/>
71 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply"> 97 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
85 <option value="LM" selected="true">LM</option> 111 <option value="LM" selected="true">LM</option>
86 <option value="CPLM">CPLM</option> 112 <option value="CPLM">CPLM</option>
87 <option value="NEGBIN">NEGBIN</option> 113 <option value="NEGBIN">NEGBIN</option>
88 <option value="ZINB">ZINB</option> 114 <option value="ZINB">ZINB</option>
89 </param> 115 </param>
90 <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/> 116 <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>
119 <option value="BY">Benjamini-Yekutieli(BY)</option>
120 </param>
91 <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"/> 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"/>
92 </section> 122 </section>
93 <section name="output" title="Set Plotting Output" expanded="true"> 123 <section name="output" title="Set Plotting Output" expanded="true">
94 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/> 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"/>
95 <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"/> 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"/>
113 </outputs> 143 </outputs>
114 <tests> 144 <tests>
115 <test expect_num_outputs="5"> 145 <test expect_num_outputs="5">
116 <param name="input_data" value="HMP2_taxonomy.tsv"/> 146 <param name="input_data" value="HMP2_taxonomy.tsv"/>
117 <param name="input_metadata" value="HMP2_metadata.tsv"/> 147 <param name="input_metadata" value="HMP2_metadata.tsv"/>
118 <param name="random_effects" value="site,subject"/> 148 <param name="random_effects" value= "2,5"/>
119 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age"/> 149 <param name="fixed_effects" value="4,9,10,11,6,3"/>
120 <section name="additional_options"> 150 <section name="additional_options">
121 <param name="min_abundance" value="0.0"/> 151 <param name="min_abundance" value="0.0"/>
122 <param name="min_prevalence" value="0.1"/> 152 <param name="min_prevalence" value="0.1"/>
123 <param name="max_significance" value="0.25"/> 153 <param name="max_significance" value="0.25"/>
124 <param name="normalization" value="NONE"/> 154 <param name="normalization" value="NONE"/>
196 </output_collection> 226 </output_collection>
197 </test> 227 </test>
198 <test expect_num_outputs="5"> 228 <test expect_num_outputs="5">
199 <param name="input_data" value="HMP2_taxonomy.tsv"/> 229 <param name="input_data" value="HMP2_taxonomy.tsv"/>
200 <param name="input_metadata" value="HMP2_metadata.tsv"/> 230 <param name="input_metadata" value="HMP2_metadata.tsv"/>
201 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> 231 <param name="fixed_effects" value="4,9"/>
202 <section name="additional_options"> 232 <section name="additional_options">
203 <param name="min_abundance" value="0.0"/> 233 <param name="min_abundance" value="0.0"/>
204 <param name="min_prevalence" value="0.1"/> 234 <param name="min_prevalence" value="0.1"/>
205 <param name="max_significance" value="0.25"/> 235 <param name="max_significance" value="0.25"/>
206 <param name="normalization" value="NONE"/> 236 <param name="normalization" value="NONE"/>
243 </output_collection> 273 </output_collection>
244 </test> 274 </test>
245 <test expect_num_outputs="5"> 275 <test expect_num_outputs="5">
246 <param name="input_data" value="HMP2_taxonomy.tsv"/> 276 <param name="input_data" value="HMP2_taxonomy.tsv"/>
247 <param name="input_metadata" value="HMP2_metadata.tsv"/> 277 <param name="input_metadata" value="HMP2_metadata.tsv"/>
248 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> 278 <param name="fixed_effects" value="4,9"/>
249 <section name="additional_options"> 279 <section name="additional_options">
250 <param name="min_abundance" value="0.0001"/> 280 <param name="min_abundance" value="0.0001"/>
251 <param name="min_prevalence" value="0.1"/> 281 <param name="min_prevalence" value="0.1"/>
252 <param name="max_significance" value="0.25"/> 282 <param name="max_significance" value="0.25"/>
253 <param name="normalization" value="NONE"/> 283 <param name="normalization" value="NONE"/>
302 <has_size value="2599373" delta="1000000" /> 332 <has_size value="2599373" delta="1000000" />
303 </assert_contents> 333 </assert_contents>
304 </element> 334 </element>
305 </output_collection> 335 </output_collection>
306 </test> 336 </test>
337 <test expect_num_outputs="5">
338 <param name="input_data" value="HMP2_taxonomy.tsv"/>
339 <param name="input_metadata" value="HMP2_metadata.tsv"/>
340 <param name="random_effects" value="3" />
341 <section name="additional_options">
342 <param name="min_abundance" value="0.0"/>
343 <param name="min_prevalence" value="0.1"/>
344 <param name="max_significance" value="0.25"/>
345 <param name="normalization" value="TSS"/>
346 <param name="transform" value="LOG"/>
347 <param name="analysis_method" value="LM"/>
348 <param name="correction" value="BY"/>
349 <param name="standardize" value="True"/>
350 </section>
351 <section name="output">
352 <param name="plot_heatmap" value="true"/>
353 <param name="heatmap_first_n" value="50"/>
354 <param name="plot_scatter" value="true"/>
355 <param name="residuals_output" value="true"/>
356 </section>
357 <output name="all_results">
358 <assert_contents>
359 <has_text text="feature"/>
360 <has_n_lines n="8092"/>
361 <has_n_columns n="9"/>
362 </assert_contents>
363 </output>
364 <output name="significant_results">
365 <assert_contents>
366 <has_text text="subject"/>
367 <has_n_lines n="216" delta="5"/>
368 <has_n_columns n="9"/>
369 </assert_contents>
370 </output>
371 <output name="residuals">
372 <assert_contents>
373 <has_size value="671142" delta="1000"/>
374 </assert_contents>
375 </output>
376 <output_collection name="figures_pdfs" type="list">
377 <element name="heatmap.pdf" ftype="pdf">
378 <assert_contents>
379 <has_size value="7000" delta="1000" />
380 </assert_contents>
381 </element>
382 </output_collection>
383 </test>
384 <test expect_num_outputs="5">
385 <param name="input_data" value="HMP2_taxonomy.tsv"/>
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>
307 </tests> 431 </tests>
308 <help><![CDATA[ 432 <help><![CDATA[
309 @HELP_HEADER@ 433 @HELP_HEADER@
310 MaAsLin 2 434 MaAsLin 2
311 ========= 435 =========
345 - Q-values smaller than or equal to the threshold (tabular file) 469 - Q-values smaller than or equal to the threshold (tabular file)
346 - This file is a subset of the results in the first file. 470 - This file is a subset of the results in the first file.
347 - It only includes associations with q-values <= to the threshold. 471 - It only includes associations with q-values <= to the threshold.
348 - Data frame with residuals for each feature (R data file) 472 - Data frame with residuals for each feature (R data file)
349 - This file contains a data frame with residuals for each feature. 473 - This file contains a data frame with residuals for each feature.
474
475 Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
476
350 2- Visualization output files 477 2- Visualization output files
351 - Heatmap of the significant associations (PDF file) 478 - Heatmap of the significant associations (PDF file)
352 - This file contains a heatmap of the significant associations. 479 - This file contains a heatmap of the significant associations.
353 - A plot for every significant association found (PDF file(s)) 480 - A plot for every significant association found (PDF file(s))
354 - A plot is generated for each significant association. 481 - A plot is generated for each significant association.