Mercurial > repos > iuc > dimet_enrichment_plot

comparison macros.xml @ 2:2de209fb390b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
author iuc
date Thu, 15 Feb 2024 12:52:26 +0000
parents 79720105f8c0
children c6879530205c
comparison
equal deleted inserted replaced
1:79720105f8c0 2:2de209fb390b
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.1.4</token> 2 <token name="@TOOL_VERSION@">0.2.1</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@EXECUTABLE@">pca</token> 4 <token name="@EXECUTABLE@">pca</token>
5 <xml name="factor_repeat">
6 <repeat name="rep_factorName" title="Factor" min="1">
7 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"
8 help="Only letters, numbers and underscores will be retained in this field">
9 <sanitizer>
10 <valid initial="string.letters,string.digits"><add value="_" /></valid>
11 </sanitizer>
12 </param>
13 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">
14 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"
15 help="Only letters, numbers and underscores will be retained in this field">
16 <sanitizer>
17 <valid initial="string.letters,string.digits"><add value="_" /></valid>
18 </sanitizer>
19 </param>
20 <yield/>
21 </repeat>
22 </repeat>
23 </xml>
24 <xml name="requirements"> 5 <xml name="requirements">
25 <requirements> 6 <requirements>
26 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
27 </requirements> 8 </requirements>
28 </xml> 9 </xml>
10 <xml name="statistical_test_for_multigroup">
11 <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
12 <option value="KW">Kruskal-Wallis</option>
13 </param>
14 </xml>
29 <xml name="statistical_test"> 15 <xml name="statistical_test">
30 <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> 16 <conditional name="statistics">
31 <option value="Tt">t-test</option> 17 <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform">
32 <option value="MW">Mann Whitney</option> 18 <option value="parametric">parametric</option>
33 <option value="KW">Kruskall Wallis</option> 19 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>
34 <option value="ranksum">Wilcoxon's rank sum test</option> 20 <option value="non-parametric-distribution">non-parametric (distribution based)</option>
35 <option value="Wcox">Wilcoxon signed-rank test</option> 21 </param>
36 <option value="BrMu">Brunner-Munzel test</option> 22 <when value="parametric">
37 <option value="prm-scipy">permutations test</option> 23 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
38 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option> 24 <option value="Tt" selected="true">t-test</option>
39 </param> 25 </param>
26 </when>
27 <when value="non-parametric-rank">
28 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
29 <option value="MW">Mann Whitney</option>
30 <option value="KW">Kruskal-Wallis</option>
31 <option value="ranksum" selected="true">Wilcoxon's rank sum test</option>
32 <option value="Wcox">Wilcoxon signed-rank test</option>
33 <option value="BrMu">Brunner-Munzel test</option>
34 </param>
35 </when>
36 <when value="non-parametric-distribution">
37 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">
38 <option value="prm-scipy" selected="true">permutations test</option>
39 <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>
40 </param>
41 </when>
42 </conditional>
43
40 </xml> 44 </xml>
41 <xml name="citations"> 45 <xml name="citations">
42 <citations> 46 <citations>
43 <citation type="bibtex"> 47 <citation type="bibtex">
44 @software{Galvis_Rodriguez_DIMet, 48 @software{Galvis_Rodriguez_DIMet,
84 <expand macro="isotopologue_prop_file_macros"/> 88 <expand macro="isotopologue_prop_file_macros"/>
85 <expand macro="metadata_file_macros"/> 89 <expand macro="metadata_file_macros"/>
86 </xml> 90 </xml>
87 <xml name="input_parameters_metabologram"> 91 <xml name="input_parameters_metabologram">
88 <conditional name="data_input"> 92 <conditional name="data_input">
89 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance, mean enrichment or isotopologue files"> 93 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files">
90 <option value="abundance" selected="True">abundance</option> 94 <option value="abundance" selected="True">abundance</option>
91 <option value="mean_enrichment">mean_enrichment</option> 95 <option value="mean_enrichment">mean_enrichment</option>
92 </param> 96 </param>
93 <when value="abundance"> 97 <when value="abundance">
94 <expand macro="abundance_file_macros"/> 98 <expand macro="abundance_file_macros"/>
95 <param name="metabolites_list" type="select" optional="false" multiple="true" 99 <param name="metabolites_list" type="select" optional="false" multiple="true"
96 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> 100 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
97 <validator type="length" min="1" message="Please enter at max 2 compartments"/> 101 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
98 <options from_dataset="abundance_file"> 102 <options from_dataset="abundance_file">
99 <column name="metabolite_or_isotopologue" index="0"/> 103 <column name="metabolite_or_isotopologue" index="0"/>
100 <column name="value" index="0"/> 104 <column name="value" index="0"/>
101 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> 105 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
113 <expand macro="statistical_test"/> 117 <expand macro="statistical_test"/>
114 </when> 118 </when>
115 <when value="mean_enrichment"> 119 <when value="mean_enrichment">
116 <expand macro="enrichment_file_macros"/> 120 <expand macro="enrichment_file_macros"/>
117 <param name="metabolites_list" type="select" optional="false" multiple="true" 121 <param name="metabolites_list" type="select" optional="false" multiple="true"
118 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> 122 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
119 <validator type="length" min="1" message="Please enter at max 2 compartments"/> 123 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
120 <options from_dataset="me_or_frac_contrib_file"> 124 <options from_dataset="me_or_frac_contrib_file">
121 <column name="metabolite_or_isotopologue" index="0"/> 125 <column name="metabolite_or_isotopologue" index="0"/>
122 <column name="value" index="0"/> 126 <column name="value" index="0"/>
123 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> 127 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
137 </conditional> 141 </conditional>
138 <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/> 142 <param name="path_kegg_metabolites" type="data" format="tabular" label="Pathways kegg metabolites file" help="A file with the pathways and respective metabolites ID, that must match with those in your metabolomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
139 <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/> 143 <param name="path_kegg_transcripts" type="data" format="tabular" label="Pathways kegg transcripts file" help="A file with the pathways and respective gene symbols, which must match with those present in the transcriptomics data. The names of the columns must be the pathways' names, see the minimal data example downloaded from zenodo as explained above. (see help below for more details)"/>
140 <expand macro="metadata_file_macros"/> 144 <expand macro="metadata_file_macros"/>
141 </xml> 145 </xml>
146 <xml name="input_parameters_bivar_analysis">
147 <conditional name="data_input">
148 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
149 <option value="abundance" selected="True">abundance</option>
150 <option value="mean_enrichment">mean_enrichment</option>
151 <option value="isotop_prop">isotop_prop</option>
152 <option value="isotop_abs">isotop_abs</option>
153 </param>
154 <when value="abundance">
155 <expand macro="abundance_file_macros"/>
156
157 </when>
158 <when value="mean_enrichment">
159 <expand macro="enrichment_file_macros"/>
160 </when>
161 <when value="isotop_prop">
162 <expand macro="isotopologue_prop_file_macros"/>
163 </when>
164 <when value="isotop_abs">
165 <expand macro="isotopologue_abs_file_macros"/>
166 </when>
167 </conditional>
168 <expand macro="metadata_file_macros"/>
169 </xml>
142 <xml name="input_parameters_diff_analysis"> 170 <xml name="input_parameters_diff_analysis">
143 <conditional name="data_input"> 171 <conditional name="data_input">
144 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues count files" help="Select between raw abundance and mean enrichment files"> 172 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
145 <option value="abundance" selected="True">abundance</option> 173 <option value="abundance" selected="True">abundance</option>
146 <option value="mean_enrichment">mean_enrichment</option> 174 <option value="mean_enrichment">mean_enrichment</option>
147 <option value="isotop_prop">isotop_prop</option> 175 <option value="isotop_prop">isotop_prop</option>
148 <option value="isotop_abs">isotop_abs</option> 176 <option value="isotop_abs">isotop_abs</option>
149 </param> 177 </param>
165 <expand macro="statistical_test"/> 193 <expand macro="statistical_test"/>
166 </when> 194 </when>
167 </conditional> 195 </conditional>
168 <expand macro="metadata_file_macros"/> 196 <expand macro="metadata_file_macros"/>
169 </xml> 197 </xml>
198 <xml name="input_parameters_multi_diff_analysis">
199 <conditional name="data_input">
200 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance, mean enrichment or isotopologue files">
201 <option value="abundance" selected="True">abundance</option>
202 <option value="mean_enrichment">mean_enrichment</option>
203 <option value="isotop_prop">isotop_prop</option>
204 <option value="isotop_abs">isotop_abs</option>
205 </param>
206 <when value="abundance">
207 <expand macro="abundance_file_macros"/>
208 <expand macro="statistical_test_for_multigroup"/>
209
210 </when>
211 <when value="mean_enrichment">
212 <expand macro="enrichment_file_macros"/>
213 <expand macro="statistical_test_for_multigroup"/>
214 </when>
215 <when value="isotop_prop">
216 <expand macro="isotopologue_prop_file_macros"/>
217 <expand macro="statistical_test_for_multigroup"/>
218 </when>
219 <when value="isotop_abs">
220 <expand macro="isotopologue_abs_file_macros"/>
221 <expand macro="statistical_test_for_multigroup"/>
222 </when>
223 </conditional>
224 <expand macro="metadata_file_macros"/>
225 </xml>
170 <xml name="suffix"> 226 <xml name="suffix">
171 <param name="suffix" type="text" optional="false" label="suffix to add to output files" > 227 <param name="suffix" type="text" optional="false" label="suffix to add to output files" >
172 <sanitizer invalid_char=""> 228 <sanitizer invalid_char="">
173 <valid initial="string.ascii_letters,string.digits"> 229 <valid initial="string.ascii_letters,string.digits">
174 <add value="_" /> 230 <add value="_" />
175 </valid> 231 </valid>
176 </sanitizer> 232 </sanitizer>
177 </param> 233 </param>
178 </xml> 234 </xml>
179 <xml name="conditions"> 235 <xml name="conditions">
180 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to metabolite list"> 236 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
181 <options from_dataset="metadata_path"> 237 <options from_dataset="metadata_path">
182 <column name="condition" index="1"/> 238 <column name="condition" index="1"/>
183 <column name="value" index="1"/> 239 <column name="value" index="1"/>
184 <filter type="unique_value" name="condition" column="condition"/> 240 <filter type="unique_value" name="condition" column="condition"/>
185 <filter type="remove_value" value="condition"/> 241 <filter type="remove_value" value="condition"/>
230 </valid> 286 </valid>
231 </sanitizer> 287 </sanitizer>
232 </param> 288 </param>
233 </xml> 289 </xml>
234 <xml name="timepoint"> 290 <xml name="timepoint">
235 <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if two conditions are set.)"> 291 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)">
236 <options from_dataset="metadata_path"> 292 <options from_dataset="metadata_path">
237 <column name="timepoint" index="2"/> 293 <column name="timepoint" index="2"/>
238 <column name="value" index="2"/> 294 <column name="value" index="2"/>
239 <filter type="unique_value" name="timepoint" column="2"/> 295 <filter type="unique_value" name="timepoint" column="2"/>
240 <filter type="remove_value" value="timepoint"/> 296 <filter type="remove_value" value="timepoint"/>
305 <remove value="&apos;"/> 361 <remove value="&apos;"/>
306 </valid> 362 </valid>
307 </sanitizer> 363 </sanitizer>
308 </param> 364 </param>
309 </xml> 365 </xml>
366 <xml name="compartments_metabologram">
367 <param name="compartments" type="select" optional="false" multiple="false"
368 label="Browse compartments from metadata file (1 max.). You have to load a metadata file prior to have access to compartments">
369 <options from_dataset="metadata_path">
370 <column name="compartment" index="4"/>
371 <column name="value" index="4"/>
372 <filter type="unique_value" name="compartment" column="4"/>
373 <filter type="remove_value" value="compartment"/>
374 </options>
375 <sanitizer>
376 <valid initial="default">
377 <add preset="string.printable"/>
378 <add value="\t"/>
379 <remove value="&quot;"/>
380 <remove value="&apos;"/>
381 </valid>
382 </sanitizer>
383 </param>
384 </xml>
310 <xml name="compartments"> 385 <xml name="compartments">
311 <param name="compartments" type="select" optional="false" multiple="true" 386 <param name="compartments" type="select" optional="false" multiple="true"
312 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments"> 387 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments">
313 <options from_dataset="metadata_path"> 388 <options from_dataset="metadata_path">
314 <column name="compartment" index="4"/> 389 <column name="compartment" index="4"/>
326 </sanitizer> 401 </sanitizer>
327 </param> 402 </param>
328 </xml> 403 </xml>
329 <xml name="abundance_metabolites_list"> 404 <xml name="abundance_metabolites_list">
330 <param name="metabolites_list" type="select" optional="false" multiple="true" 405 <param name="metabolites_list" type="select" optional="false" multiple="true"
331 label="Select Metabolite(s) for factor 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list"> 406 label="Select Metabolite(s) for condition 1 to plot (1 min). You have to load a abundance file prior to have access to metabolite list">
332 <validator type="length" min="1" message="Please enter at max 2 compartments"/> 407 <validator type="length" min="1" message="Please enter at max 2 compartments"/>
333 <options from_dataset="abundance_file"> 408 <options from_dataset="abundance_file">
334 <column name="metabolite_or_isotopologue" index="0"/> 409 <column name="metabolite_or_isotopologue" index="0"/>
335 <column name="value" index="0"/> 410 <column name="value" index="0"/>
336 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> 411 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/>
346 </sanitizer> 421 </sanitizer>
347 </param> 422 </param>
348 </xml> 423 </xml>
349 <xml name="enrichment_metabolites_list"> 424 <xml name="enrichment_metabolites_list">
350 <param name="metabolites_list" type="select" optional="false" multiple="true" 425 <param name="metabolites_list" type="select" optional="false" multiple="true"
351 label="Select Metabolite(s) for factor 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> 426 label="Select Metabolite(s) for condition 1 to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
352 <validator type="length" min="1" message="Please enter at max 2 compartments"/> 427 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
353 <options from_dataset="me_or_frac_contrib_file"> 428 <options from_dataset="me_or_frac_contrib_file">
354 <column name="ID" index="0"/> 429 <column name="ID" index="0"/>
355 <column name="value" index="0"/> 430 <column name="value" index="0"/>
356 <filter type="unique_value" name="ID" column="0"/> 431 <filter type="unique_value" name="ID" column="0"/>
357 <filter type="remove_value" value="ID"/> 432 <filter type="remove_value" value="ID"/>
367 </param> 442 </param>
368 </xml> 443 </xml>
369 <xml name="isotopologue_metabolites_list"> 444 <xml name="isotopologue_metabolites_list">
370 <param name="metabolites_list" type="select" optional="false" multiple="true" 445 <param name="metabolites_list" type="select" optional="false" multiple="true"
371 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> 446 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list">
372 <validator type="length" min="1" message="Please enter at max 2 compartments"/> 447 <validator type="length" min="1" message="Please enter at min 1 metabolite"/>
373 <options from_dataset="isotop_prop_file"> 448 <options from_dataset="isotop_prop_file">
374 <column name="ID" index="0"/> 449 <column name="ID" index="0"/>
375 <column name="value" index="0"/> 450 <column name="value" index="0"/>
376 <filter type="unique_value" name="ID" column="0"/> 451 <filter type="unique_value" name="ID" column="0"/>
377 <filter type="remove_value" value="ID"/> 452 <filter type="remove_value" value="ID"/>
385 </valid> 460 </valid>
386 </sanitizer> 461 </sanitizer>
387 </param> 462 </param>
388 </xml> 463 </xml>
389 <xml name="deg_list"> 464 <xml name="deg_list">
390 <repeat name="deg_list" title="Deregulated gene set"> 465 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1">
391 <param name="input" type="data" format="tabular" label="Deregulated genes set"/> 466 <param name="input" type="data" format="tabular" label="Deregulated genes set"/>
392 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/> 467 <param name="idcol" type="data_column" data_ref="input" label="Column for id" use_header_names="true"/>
393 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/> 468 <param name="valuecol" type="data_column" data_ref="input" label="Column for values" use_header_names="true"/>
469 <param name="timepoint" type="select" optional="false" multiple="false" label="Browse timepoint from metadata file (1 min.)">
470 <options from_dataset="metadata_path">
471 <column name="timepoint" index="2"/>
472 <column name="value" index="2"/>
473 <filter type="unique_value" name="timepoint" column="2"/>
474 <filter type="remove_value" value="timepoint"/>
475 <filter type="sort_by" name="timepoint" column="1"/>
476 </options>
477 <sanitizer>
478 <valid initial="default">
479 <add preset="string.printable"/>
480 <add value="\t"/>
481 <remove value="&quot;"/>
482 <remove value="&apos;"/>
483 </valid>
484 </sanitizer>
485 </param>
486 <repeat name="factor_list" title="Conditions" default="2" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list">
487 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
488 <options from_dataset="metadata_path">
489 <column name="condition" index="1"/>
490 <column name="value" index="1"/>
491 <filter type="unique_value" name="condition" column="condition"/>
492 <filter type="remove_value" value="condition"/>
493 </options>
494 <sanitizer>
495 <valid initial="default">
496 <add preset="string.printable"/>
497 <add value="\t"/>
498 <remove value="&quot;"/>
499 <remove value="&apos;"/>
500 </valid>
501 </sanitizer>
502 </param>
503 </repeat>
504
394 </repeat> 505 </repeat>
506 </xml>
507 <xml name="plot_abundance_factor_list">
508 <repeat name="plot_abundance_factor_list" title="Conditions" min="1" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
509 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
510 <options from_dataset="metadata_path">
511 <column name="condition" index="1"/>
512 <column name="value" index="1"/>
513 <filter type="unique_value" name="condition" column="condition"/>
514 <filter type="remove_value" value="condition"/>
515 </options>
516 <sanitizer>
517 <valid initial="default">
518 <add preset="string.printable"/>
519 <add value="\t"/>
520 <remove value="&quot;"/>
521 <remove value="&apos;"/>
522 </valid>
523 </sanitizer>
524 </param>
525 </repeat>
526 </xml>
527 <xml name="plot_factor_list">
528 <repeat name="plot_factor_list" title="Conditions" min="2" help="Specify conditions to compare from metadata file (1 min. only if two timepoints are set. 2 max.). You have to load a metadata file prior to have access to condition list">
529 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
530 <options from_dataset="metadata_path">
531 <column name="condition" index="1"/>
532 <column name="value" index="1"/>
533 <filter type="unique_value" name="condition" column="condition"/>
534 <filter type="remove_value" value="condition"/>
535 </options>
536 <sanitizer>
537 <valid initial="default">
538 <add preset="string.printable"/>
539 <add value="\t"/>
540 <remove value="&quot;"/>
541 <remove value="&apos;"/>
542 </valid>
543 </sanitizer>
544 </param>
545 </repeat>
546 </xml>
547 <xml name="factor_list">
548 <repeat name="factor_list" title="Conditions" min="2" max="2" help="Specify conditions to compare from metadata file (for each comparison, the first specified condition is the reference). You have to load a metadata file prior to have access to condition list">
549 <param name="condition" label="Condition" type="select" optional="false" multiple="false">
550 <options from_dataset="metadata_path">
551 <column name="condition" index="1"/>
552 <column name="value" index="1"/>
553 <filter type="unique_value" name="condition" column="condition"/>
554 <filter type="remove_value" value="condition"/>
555 </options>
556 <sanitizer>
557 <valid initial="default">
558 <add preset="string.printable"/>
559 <add value="\t"/>
560 <remove value="&quot;"/>
561 <remove value="&apos;"/>
562 </valid>
563 </sanitizer>
564 </param>
565 </repeat>
566 </xml>
567 <xml name="palette">
568 <param name="palette" type="select" value="pastel" display="radio" label="Select palette colormap to apply to abundance plot." help="For more information see https://seaborn.pydata.org/tutorial/color_palettes.html">
569 <option value="pastel" selected="true">pastel</option>
570 <option value="deep">deep</option>
571 <option value="muted">muted</option>
572 <option value="bright">bright</option>
573 <option value="dark">dark</option>
574 <option value="colorblind">colorblind</option>
575 </param>
395 </xml> 576 </xml>
396 <token name="@INIT_PCA@"><![CDATA[ 577 <token name="@INIT_PCA@"><![CDATA[
397 #import json 578 #import json
398 #import re 579 #import re
399 580
400 mkdir -p data/raw && 581 mkdir -p data &&
401 mkdir -p data/processed &&
402 582
403 #if $metadata_path: 583 #if $metadata_path:
404 ln -s '$metadata_path' data/raw/metadata.csv && 584 ln -s '$metadata_path' data/metadata.csv &&
405 #end if 585 #end if
406 #if $abundance_file: 586 #if $abundance_file:
407 ln -s '$abundance_file' data/raw/abundance.csv && 587 ln -s '$abundance_file' data/abundance.csv &&
408 #end if 588 #end if
409 #if $me_or_frac_contrib_file: 589 #if $me_or_frac_contrib_file:
410 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && 590 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
411 #end if 591 #end if
412 592
413 ]]></token> 593 ]]></token>
414 <token name="@INIT_CONFIG@"><![CDATA[ 594 <token name="@INIT_CONFIG@"><![CDATA[
415 mkdir -p '$__new_file_path__/config' && 595 mkdir -p '$__new_file_path__/config' &&
418 <token name="@REMOVE_CONFIG@"><![CDATA[ 598 <token name="@REMOVE_CONFIG@"><![CDATA[
419 && rm -r '$__new_file_path__/config' 599 && rm -r '$__new_file_path__/config'
420 ]]></token> 600 ]]></token>
421 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ 601 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
422 602
423 mkdir -p data/raw && 603 mkdir -p data &&
424 mkdir -p data/processed &&
425 604
426 #if $metadata_path: 605 #if $metadata_path:
427 ln -s '$metadata_path' data/raw/metadata.csv && 606 ln -s '$metadata_path' data/metadata.csv &&
428 #end if 607 #end if
429 #if $abundance_file: 608 #if $abundance_file:
430 ln -s '$abundance_file' data/raw/abundance.csv && 609 ln -s '$abundance_file' data/abundance.csv &&
431 #end if 610 #end if
432 ]]></token> 611 ]]></token>
433 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ 612 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[
434 613
435 mkdir -p data/raw && 614 mkdir -p data &&
436 mkdir -p data/processed &&
437 615
438 #if $metadata_path: 616 #if $metadata_path:
439 ln -s '$metadata_path' data/raw/metadata.csv && 617 ln -s '$metadata_path' data/metadata.csv &&
440 #end if 618 #end if
441 #if $me_or_frac_contrib_file: 619 #if $me_or_frac_contrib_file:
442 ln -s '$me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && 620 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
443 #end if 621 #end if
444 ]]></token> 622 ]]></token>
445 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ 623 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[
446 624
447 mkdir -p data/raw && 625 mkdir -p data &&
448 mkdir -p data/processed &&
449 626
450 #if $metadata_path: 627 #if $metadata_path:
451 ln -s '$metadata_path' data/raw/metadata.csv && 628 ln -s '$metadata_path' data/metadata.csv &&
452 #end if 629 #end if
453 #if $isotop_prop_file: 630 #if $isotop_prop_file:
454 ln -s '$isotop_prop_file' data/raw/isotop_prop.csv && 631 ln -s '$isotop_prop_file' data/isotop_prop.csv &&
455 #end if 632 #end if
456 ]]></token> 633 ]]></token>
457 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[ 634 <token name="@INIT_BI_ANALYSIS@"><![CDATA[
458 635
459 mkdir -p data/raw && 636 mkdir -p data &&
460 mkdir -p data/processed &&
461 637
462 #if $metadata_path: 638 #if $metadata_path:
463 ln -s '$metadata_path' data/raw/metadata.csv && 639 ln -s '$metadata_path' data/metadata.csv &&
464 #end if 640 #end if
641 #set conditions_MDV_comparison = {}
642 #silent $conditions_MDV_comparison['isotopologue_proportions']='pearson'
643 #set timepoints_MDV_comparison = {}
644 #silent $timepoints_MDV_comparison['isotopologue_proportions']='pearson'
645 #set conditions_metabolite_time_profiles = {}
646 #silent $conditions_metabolite_time_profiles['abundances']='pearson'
647 #silent $conditions_metabolite_time_profiles['mean_enrichment']='pearson'
465 648
466 #set $impute_values = {} 649 #set $impute_values = {}
467 #if str( $data_input.data_input_selector ) == "abundance": 650 #if str( $data_input.data_input_selector ) == "abundance":
468 #if $data_input.abundance_file: 651 #if $data_input.abundance_file:
469 ln -s '$data_input.abundance_file' data/raw/abundance.csv && 652 ln -s '$data_input.abundance_file' data/abundance.csv &&
470 #silent $impute_values['abundances']='min' 653 #silent $impute_values['abundances']='min'
471 #end if 654 #end if
472 #elif str( $data_input.data_input_selector ) == "mean_enrichment": 655 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
473 #if $data_input.me_or_frac_contrib_file: 656 #if $data_input.me_or_frac_contrib_file:
474 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && 657 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
475 #silent $impute_values['mean_enrichment']='min' 658 #silent $impute_values['mean_enrichment']='min'
476 #end if 659 #end if
477 #elif str( $data_input.data_input_selector ) == "isotop_prop": 660 #elif str( $data_input.data_input_selector ) == "isotop_prop":
478 #if $data_input.isotop_prop_file: 661 #if $data_input.isotop_prop_file:
479 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && 662 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
480 #silent $impute_values['isotopologue_proportions']='min' 663 #silent $impute_values['isotopologue_proportions']='min'
481 #end if 664 #end if
482 #else 665 #else
483 #if $data_input.isotop_abs_file: 666 #if $data_input.isotop_abs_file:
484 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && 667 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
668 #silent $impute_values['isotopologues']='min'
669 #end if
670 #end if
671 ]]></token>
672 <token name="@INIT_DIFF_ANALYSIS@"><![CDATA[
673
674 mkdir -p data &&
675
676 #if $metadata_path:
677 ln -s '$metadata_path' data/metadata.csv &&
678 #end if
679
680 #set $impute_values = {}
681 #if str( $data_input.data_input_selector ) == "abundance":
682 #if $data_input.abundance_file:
683 ln -s '$data_input.abundance_file' data/abundance.csv &&
684 #silent $impute_values['abundances']='min'
685 #end if
686 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
687 #if $data_input.me_or_frac_contrib_file:
688 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
689 #silent $impute_values['mean_enrichment']='min'
690 #end if
691 #elif str( $data_input.data_input_selector ) == "isotop_prop":
692 #if $data_input.isotop_prop_file:
693 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
694 #silent $impute_values['isotopologue_proportions']='min'
695 #end if
696 #else
697 #if $data_input.isotop_abs_file:
698 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
485 #silent $impute_values['isotopologues']='min' 699 #silent $impute_values['isotopologues']='min'
486 #end if 700 #end if
487 #end if 701 #end if
488 ]]></token> 702 ]]></token>
489 <token name="@INIT_METABOLOGRAM@"><![CDATA[ 703 <token name="@INIT_METABOLOGRAM@"><![CDATA[
491 #import re 705 #import re
492 #import os 706 #import os
493 #import csv 707 #import csv
494 #import subprocess 708 #import subprocess
495 709
496 mkdir -p data/raw && 710 mkdir -p data &&
497 mkdir -p data/processed &&
498 mkdir -p data/integration_files &&
499 711
500 #if $path_kegg_metabolites: 712 #if $path_kegg_metabolites:
501 ln -s '$path_kegg_metabolites' data/integration_files/pathways_kegg_metabolites.csv && 713 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv &&
502 #end if 714 #end if
503 #if $path_kegg_transcripts: 715 #if $path_kegg_transcripts:
504 ln -s '$path_kegg_transcripts' data/integration_files/pathways_kegg_transcripts.csv && 716 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv &&
505 #end if 717 #end if
506 718
507 #if $metadata_path: 719 #if $metadata_path:
508 ln -s '$metadata_path' data/raw/metadata.csv && 720 ln -s '$metadata_path' data/metadata.csv &&
509 #end if 721 #end if
510 722
511 #set $impute_values = {} 723 #set $impute_values = {}
512 #if str( $data_input.data_input_selector ) == "abundance": 724 #if str( $data_input.data_input_selector ) == "abundance":
513 #if $data_input.abundance_file: 725 #if $data_input.abundance_file:
514 ln -s '$data_input.abundance_file' data/raw/abundance.csv && 726 ln -s '$data_input.abundance_file' data/abundance.csv &&
515 #silent $impute_values['abundances']='min' 727 #silent $impute_values['abundances']='min'
516 #end if 728 #end if
517 #else: 729 #else:
518 #if $data_input.me_or_frac_contrib_file: 730 #if $data_input.me_or_frac_contrib_file:
519 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && 731 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
520 #silent $impute_values['mean_enrichment']='min' 732 #silent $impute_values['mean_enrichment']='min'
521 #end if 733 #end if
522 #end if 734 #end if
523 735
524 #for $i, $s in enumerate($deg_list) 736 #for $i, $s in enumerate($deg_list)
525 #set $cpt = str($i+1) 737 #set $cpt = str($i+1)
526 ln -s '${s.input}' data/integration_files/DEG_comparison'${cpt}'.csv && 738 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv &&
527 #end for 739 #end for
528 740
529 741
530 ]]></token> 742 ]]></token>
531 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ 743 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[
532 744
533 mkdir -p data/raw && 745 mkdir -p data &&
534 mkdir -p data/processed &&
535 746
536 #if $metadata_path: 747 #if $metadata_path:
537 ln -s '$metadata_path' data/raw/metadata.csv && 748 ln -s '$metadata_path' data/metadata.csv &&
538 #end if 749 #end if
539 750
540 #set $impute_values = {} 751 #set $impute_values = {}
541 #if str( $data_input.data_input_selector ) == "abundance": 752 #if str( $data_input.data_input_selector ) == "abundance":
542 #if $data_input.abundance_file: 753 #if $data_input.abundance_file:
543 ln -s '$data_input.abundance_file' data/raw/abundance.csv && 754 ln -s '$data_input.abundance_file' data/abundance.csv &&
544 #silent $impute_values['abundances']='min' 755 #silent $impute_values['abundances']='min'
545 #end if 756 #end if
546 #elif str( $data_input.data_input_selector ) == "mean_enrichment": 757 #elif str( $data_input.data_input_selector ) == "mean_enrichment":
547 #if $data_input.me_or_frac_contrib_file: 758 #if $data_input.me_or_frac_contrib_file:
548 ln -s '$data_input.me_or_frac_contrib_file' data/raw/me_or_frac_contrib.csv && 759 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv &&
549 #silent $impute_values['mean_enrichment']='min' 760 #silent $impute_values['mean_enrichment']='min'
550 #end if 761 #end if
551 #elif str( $data_input.data_input_selector ) == "isotop_prop": 762 #elif str( $data_input.data_input_selector ) == "isotop_prop":
552 #if $data_input.isotop_prop_file: 763 #if $data_input.isotop_prop_file:
553 ln -s '$data_input.isotop_prop_file' data/raw/isotop_prop.csv && 764 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv &&
554 #silent $impute_values['isotopologue_proportions']='min' 765 #silent $impute_values['isotopologue_proportions']='min'
555 #end if 766 #end if
556 #else 767 #else
557 #if $data_input.isotop_abs_file: 768 #if $data_input.isotop_abs_file:
558 ln -s '$data_input.isotop_abs_file' data/raw/isotop_abs.csv && 769 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv &&
559 #silent $impute_values['isotopologues']='min' 770 #silent $impute_values['isotopologues']='min'
560 #end if 771 #end if
561 #end if 772 #end if
562 ]]></token> 773 ]]></token>
563 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[ 774 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[
617 #set $conds = list() 828 #set $conds = list()
618 #for $co in $conditions: 829 #for $co in $conditions:
619 $conds.append(re.sub('"', '', str($co))) 830 $conds.append(re.sub('"', '', str($co)))
620 #end for 831 #end for
621 ]]></token> 832 ]]></token>
833 <token name="@INIT_PLOT_CONDITIONS@"><![CDATA[
834 #set $conditions = list()
835 #for $i, $s in enumerate($plot_factor_list)
836 #set $cpt = str($i+1)
837 $conditions.append(re.sub('"', '', str($s.condition)))
838 #end for
839 ]]></token>
840 <token name="@INIT_ABUNDANCE_PLOT_CONDITIONS@"><![CDATA[
841 #set $conditions = list()
842 #for $i, $s in enumerate($plot_abundance_factor_list)
843 #set $cpt = str($i+1)
844 $conditions.append(re.sub('"', '', str($s.condition)))
845 #end for
846 ]]></token>
622 <token name="@INIT_TIMEPOINTS@"><![CDATA[ 847 <token name="@INIT_TIMEPOINTS@"><![CDATA[
623 848
624 #import re 849 #import re
625 #set $timepoints = list() 850 #set $timepoints = list()
626 #for $tp in $timepoint: 851 #for $tp in $timepoint:
639 #import re 864 #import re
640 #set $metabolites = {} 865 #set $metabolites = {}
641 #for $cp in $compartments: 866 #for $cp in $compartments:
642 #silent $metabolites[re.sub('"', '', str($cp))]=list() 867 #silent $metabolites[re.sub('"', '', str($cp))]=list()
643 #for $met in $metabolites_list: 868 #for $met in $metabolites_list:
644 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str($met))) 869 #set tmp_met=re.sub('\,', '%%',str($met))
870 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0])
871 #set tmp_met_ter=re.sub('%%', '\,',str($tmp_met_bis))
872 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter)))
645 #end for 873 #end for
646 #end for 874 #end for
647 ]]></token> 875 ]]></token>
648 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[ 876 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[
649 #set $metabolites = {} 877 #set $metabolites = {}
679 #end for 907 #end for
680 #end for 908 #end for
681 ]]></token> 909 ]]></token>
682 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[ 910 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[
683 #import re 911 #import re
684 #set $conds = list() 912 #set $conditions = list()
685 #for $co in $conditions: 913 #for $i, $s in enumerate($factor_list)
686 $conds.append(re.sub('"', '', str($co))) 914 #set $cpt = str($i+1)
687 #end for 915 $conditions.append(re.sub('"', '', str($s.condition)))
916 #end for
917
918 ]]></token>
919 <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[
920 #import re
921 #set $conditions = list()
922 #for $i, $s in enumerate($plot_factor_list)
923 #set $cpt = str($i+1)
924 $conditions.append(re.sub('"', '', str($s.condition)))
925 #end for
926 ]]></token>
927 <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[
928 #import re
929 #set $conditions = list()
930 #set $timepoints = list()
931 #set $comparisons = list()
932 #for $i, $s in enumerate($deg_list)
933 #set $cpt = str($i+1)
934 #set $comparisons_bis = list()
935 #for $j, $t in enumerate($s.factor_list)
936 #set $sub_comparisons = list()
937 #if str($t.condition) not in $conditions:
938 $conditions.append(re.sub('"', '', str($t.condition)))
939 #end if
940 $sub_comparisons.append(re.sub('"', '', str($t.condition)))
941 $sub_comparisons.append(re.sub('"', '', str($s.timepoint)))
942 $comparisons_bis.append($sub_comparisons)
943 #end for
944 $timepoints.append(re.sub('"', '', str($s.timepoint)))
945 $comparisons.append($comparisons_bis)
946 #end for
947
948
688 949
689 ]]></token> 950 ]]></token>
690 <token name="@INIT_COMPARISONS@"><![CDATA[ 951 <token name="@INIT_COMPARISONS@"><![CDATA[
691 #import re 952 #import re
692 #set $conds = list() 953 #set $conds = list()
751 $comparisons.append(re.sub('"', '', str($tp))) 1012 $comparisons.append(re.sub('"', '', str($tp)))
752 #end for 1013 #end for
753 #end if 1014 #end if
754 #end if 1015 #end if
755 ]]></token> 1016 ]]></token>
1017 <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[
1018 #import re
1019 #set $conditions = list()
1020 #for $i, $s in enumerate($factor_list)
1021 #set $cpt = str($i+1)
1022 $conditions.append(re.sub('"', '', str($s.condition)))
1023 #end for
1024
1025 #set $timepoints = list()
1026 #for $tp in $timepoint:
1027 $timepoints.append(re.sub('"', '', str($tp)))
1028 #end for
1029
1030 #set $comparisons = list()
1031 #if len($conditions) > 1:
1032 #if len($timepoints) > 0:
1033 #for $tp in $timepoint:
1034 #set $ctrl_found=False
1035 #set $ctrl=""
1036 #set $comparisons_bis = list()
1037
1038 #for $co in $conditions:
1039 #set $sub_comparisons = list()
1040 #if str($co) in ["'Control'", "'control'", "'ctrl'"]:
1041 #set $ctrl_found=True
1042 #set $ctrl=str($co)
1043 #else:
1044 $sub_comparisons.append(re.sub('"', '', str($co)))
1045 $sub_comparisons.append(re.sub('"', '', str($tp)))
1046
1047 #end if
1048 $comparisons_bis.append($sub_comparisons)
1049 #end for
1050
1051 #if $ctrl_found:
1052 $sub_comparisons.append(str($ctrl))
1053 $sub_comparisons.append(str($tp))
1054 $comparisons_bis.append($sub_comparisons)
1055 #end if
1056
1057 $comparisons.append($comparisons_bis)
1058 #end for
1059 #else
1060 #for $co in $conditions:
1061 $comparisons.append(re.sub('"', '', str($co)))
1062 #end for
1063 #end if
1064
1065 #else
1066 #if len($conditions) > 0:
1067 #if len($timepoints) > 1:
1068 #for $co in $conditions:
1069 #set $comparisons_bis = list()
1070 #for $tp in $timepoint:
1071 #set $sub_comparisons = list()
1072 $sub_comparisons.append(re.sub('"', '', str($co)))
1073 $sub_comparisons.append(re.sub('"', '', str($tp)))
1074 $comparisons_bis.append($sub_comparisons)
1075 #end for
1076 $comparisons.append($comparisons_bis)
1077 #end for
1078 #end if
1079 #else
1080 #for $tp in $timepoint:
1081 $comparisons.append(re.sub('"', '', str($tp)))
1082 #end for
1083 #end if
1084 #end if
1085 ]]></token>
756 <token name="@INIT_TRANSCRIPTS@"><![CDATA[ 1086 <token name="@INIT_TRANSCRIPTS@"><![CDATA[
757 #import re 1087 #import re
758 #import os 1088 #import os
759 #import subprocess 1089 #import subprocess
760 #set $transcripts = list() 1090 #set $transcripts = list()