Mercurial > repos > iuc > dimet_bivariate_analysis
comparison macros.xml @ 0:89e637c99bed draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f
| author | iuc |
|---|---|
| date | Thu, 15 Feb 2024 12:53:48 +0000 |
| parents | |
| children | 265543358207 |
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| -1:000000000000 | 0:89e637c99bed |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">0.2.1</token> | |
| 3 <token name="@VERSION_SUFFIX@">1</token> | |
| 4 <token name="@EXECUTABLE@">pca</token> | |
| 5 <xml name="requirements"> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="@TOOL_VERSION@">dimet</requirement> | |
| 8 </requirements> | |
| 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> | |
| 15 <xml name="statistical_test"> | |
| 16 <conditional name="statistics"> | |
| 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"> | |
| 18 <option value="parametric">parametric</option> | |
| 19 <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option> | |
| 20 <option value="non-parametric-distribution">non-parametric (distribution based)</option> | |
| 21 </param> | |
| 22 <when value="parametric"> | |
| 23 <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file"> | |
| 24 <option value="Tt" selected="true">t-test</option> | |
| 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 | |
| 44 </xml> | |
| 45 <xml name="citations"> | |
| 46 <citations> | |
| 47 <citation type="bibtex"> | |
| 48 @software{Galvis_Rodriguez_DIMet, | |
| 49 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha}, | |
| 50 license = {MIT}, | |
| 51 title = {{DIMet}}, | |
| 52 url = {https://github.com/cbib/DIMet} | |
| 53 } | |
| 54 | |
| 55 </citation> | |
| 56 </citations> | |
| 57 | |
| 58 </xml> | |
| 59 <xml name="metadata_file_macros"> | |
| 60 <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures' files. This is compulsory, see section Metadata File Information."/> | |
| 61 </xml> | |
| 62 <xml name="abundance_file_macros"> | |
| 63 <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> | |
| 64 </xml> | |
| 65 <xml name="enrichment_file_macros"> | |
| 66 <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the metabolites. - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/> | |
| 67 </xml> | |
| 68 <xml name="isotopologue_prop_file_macros"> | |
| 69 <param name="isotop_prop_file" type="data" format="tabular" label="Isotopologues proportion abundance file" help=" The isotopologue proportions file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> | |
| 70 </xml> | |
| 71 <xml name="isotopologue_abs_file_macros"> | |
| 72 <param name="isotop_abs_file" type="data" format="tabular" label="Isotopologues absolute abundance file" help="The isotopologue absolute values file must be organized as a matrix: - The first column must contain isotopologues IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples. - The rows correspond to the isotopologues. - The values must be tab separated, with the first row containing the sample/column labels (see help below for more details)."/> | |
| 73 </xml> | |
| 74 <xml name="input_parameters_pca"> | |
| 75 <expand macro="abundance_file_macros"/> | |
| 76 <param name="me_or_frac_contrib_file" type="data" optional="true" format="tabular" label="Mean enrichment or fraction contribution file"/> | |
| 77 <expand macro="metadata_file_macros"/> | |
| 78 </xml> | |
| 79 <xml name="input_parameters_abundance"> | |
| 80 <expand macro="abundance_file_macros"/> | |
| 81 <expand macro="metadata_file_macros"/> | |
| 82 </xml> | |
| 83 <xml name="input_parameters_enrichment"> | |
| 84 <expand macro="enrichment_file_macros"/> | |
| 85 <expand macro="metadata_file_macros"/> | |
| 86 </xml> | |
| 87 <xml name="input_parameters_isotopologue"> | |
| 88 <expand macro="isotopologue_prop_file_macros"/> | |
| 89 <expand macro="metadata_file_macros"/> | |
| 90 </xml> | |
| 91 <xml name="input_parameters_metabologram"> | |
| 92 <conditional name="data_input"> | |
| 93 <param name="data_input_selector" type="select" label="Abundance, Enrichment or Isotopologues quantification files" help="Select between raw abundance and mean enrichment files"> | |
| 94 <option value="abundance" selected="True">abundance</option> | |
| 95 <option value="mean_enrichment">mean_enrichment</option> | |
| 96 </param> | |
| 97 <when value="abundance"> | |
| 98 <expand macro="abundance_file_macros"/> | |
| 99 <param name="metabolites_list" type="select" optional="false" multiple="true" | |
| 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"> | |
| 101 <validator type="length" min="1" message="Please enter at max 2 compartments"/> | |
| 102 <options from_dataset="abundance_file"> | |
| 103 <column name="metabolite_or_isotopologue" index="0"/> | |
| 104 <column name="value" index="0"/> | |
| 105 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> | |
| 106 <filter type="remove_value" value="metabolite_or_isotopologue"/> | |
| 107 </options> | |
| 108 <sanitizer> | |
| 109 <valid initial="default"> | |
| 110 <add preset="string.printable"/> | |
| 111 <add value="\t"/> | |
| 112 <remove value="""/> | |
| 113 <remove value="'"/> | |
| 114 </valid> | |
| 115 </sanitizer> | |
| 116 </param> | |
| 117 <expand macro="statistical_test"/> | |
| 118 </when> | |
| 119 <when value="mean_enrichment"> | |
| 120 <expand macro="enrichment_file_macros"/> | |
| 121 <param name="metabolites_list" type="select" optional="false" multiple="true" | |
| 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"> | |
| 123 <validator type="length" min="1" message="Please enter at max 2 compartments"/> | |
| 124 <options from_dataset="me_or_frac_contrib_file"> | |
| 125 <column name="metabolite_or_isotopologue" index="0"/> | |
| 126 <column name="value" index="0"/> | |
| 127 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> | |
| 128 <filter type="remove_value" value="metabolite_or_isotopologue"/> | |
| 129 </options> | |
| 130 <sanitizer> | |
| 131 <valid initial="default"> | |
| 132 <add preset="string.printable"/> | |
| 133 <add value="\t"/> | |
| 134 <remove value="""/> | |
| 135 <remove value="'"/> | |
| 136 </valid> | |
| 137 </sanitizer> | |
| 138 </param> | |
| 139 <expand macro="statistical_test"/> | |
| 140 </when> | |
| 141 </conditional> | |
| 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)"/> | |
| 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)"/> | |
| 144 <expand macro="metadata_file_macros"/> | |
| 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> | |
| 170 <xml name="input_parameters_diff_analysis"> | |
| 171 <conditional name="data_input"> | |
| 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"> | |
| 173 <option value="abundance" selected="True">abundance</option> | |
| 174 <option value="mean_enrichment">mean_enrichment</option> | |
| 175 <option value="isotop_prop">isotop_prop</option> | |
| 176 <option value="isotop_abs">isotop_abs</option> | |
| 177 </param> | |
| 178 <when value="abundance"> | |
| 179 <expand macro="abundance_file_macros"/> | |
| 180 <expand macro="statistical_test"/> | |
| 181 | |
| 182 </when> | |
| 183 <when value="mean_enrichment"> | |
| 184 <expand macro="enrichment_file_macros"/> | |
| 185 <expand macro="statistical_test"/> | |
| 186 </when> | |
| 187 <when value="isotop_prop"> | |
| 188 <expand macro="isotopologue_prop_file_macros"/> | |
| 189 <expand macro="statistical_test"/> | |
| 190 </when> | |
| 191 <when value="isotop_abs"> | |
| 192 <expand macro="isotopologue_abs_file_macros"/> | |
| 193 <expand macro="statistical_test"/> | |
| 194 </when> | |
| 195 </conditional> | |
| 196 <expand macro="metadata_file_macros"/> | |
| 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> | |
| 226 <xml name="suffix"> | |
| 227 <param name="suffix" type="text" optional="false" label="suffix to add to output files" > | |
| 228 <sanitizer invalid_char=""> | |
| 229 <valid initial="string.ascii_letters,string.digits"> | |
| 230 <add value="_" /> | |
| 231 </valid> | |
| 232 </sanitizer> | |
| 233 </param> | |
| 234 </xml> | |
| 235 <xml name="conditions"> | |
| 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"> | |
| 237 <options from_dataset="metadata_path"> | |
| 238 <column name="condition" index="1"/> | |
| 239 <column name="value" index="1"/> | |
| 240 <filter type="unique_value" name="condition" column="condition"/> | |
| 241 <filter type="remove_value" value="condition"/> | |
| 242 </options> | |
| 243 <sanitizer> | |
| 244 <valid initial="default"> | |
| 245 <add preset="string.printable"/> | |
| 246 <add value="\t"/> | |
| 247 <remove value="""/> | |
| 248 <remove value="'"/> | |
| 249 </valid> | |
| 250 </sanitizer> | |
| 251 </param> | |
| 252 </xml> | |
| 253 <xml name="conditions_multigroup"> | |
| 254 <param name="conditions" type="select" optional="false" multiple="true" label="Browse conditions from metadata file. (1 min. only if three timepoints are set). You have to load a metadata file prior to have access to conditions"> | |
| 255 <options from_dataset="metadata_path"> | |
| 256 <column name="condition" index="1"/> | |
| 257 <column name="value" index="1"/> | |
| 258 <filter type="unique_value" name="condition" column="condition"/> | |
| 259 <filter type="remove_value" value="condition"/> | |
| 260 </options> | |
| 261 <sanitizer> | |
| 262 <valid initial="default"> | |
| 263 <add preset="string.printable"/> | |
| 264 <add value="\t"/> | |
| 265 <remove value="""/> | |
| 266 <remove value="'"/> | |
| 267 </valid> | |
| 268 </sanitizer> | |
| 269 </param> | |
| 270 </xml> | |
| 271 <xml name="timepoint_multigroup"> | |
| 272 <param name="timepoint" type="select" optional="true" multiple="true" label="Browse timepoint from metadata file (1 min. only if three conditions are set). You have to load a metadata file prior to have access to conditions"> | |
| 273 <options from_dataset="metadata_path"> | |
| 274 <column name="timepoint" index="2"/> | |
| 275 <column name="value" index="2"/> | |
| 276 <filter type="unique_value" name="timepoint" column="2"/> | |
| 277 <filter type="remove_value" value="timepoint"/> | |
| 278 <filter type="sort_by" name="timepoint" column="1"/> | |
| 279 </options> | |
| 280 <sanitizer> | |
| 281 <valid initial="default"> | |
| 282 <add preset="string.printable"/> | |
| 283 <add value="\t"/> | |
| 284 <remove value="""/> | |
| 285 <remove value="'"/> | |
| 286 </valid> | |
| 287 </sanitizer> | |
| 288 </param> | |
| 289 </xml> | |
| 290 <xml name="timepoint"> | |
| 291 <param name="timepoint" type="select" optional="false" multiple="true" label="Browse timepoint from metadata file (1 min.)"> | |
| 292 <options from_dataset="metadata_path"> | |
| 293 <column name="timepoint" index="2"/> | |
| 294 <column name="value" index="2"/> | |
| 295 <filter type="unique_value" name="timepoint" column="2"/> | |
| 296 <filter type="remove_value" value="timepoint"/> | |
| 297 <filter type="sort_by" name="timepoint" column="1"/> | |
| 298 </options> | |
| 299 <sanitizer> | |
| 300 <valid initial="default"> | |
| 301 <add preset="string.printable"/> | |
| 302 <add value="\t"/> | |
| 303 <remove value="""/> | |
| 304 <remove value="'"/> | |
| 305 </valid> | |
| 306 </sanitizer> | |
| 307 </param> | |
| 308 </xml> | |
| 309 <xml name="grouping"> | |
| 310 <param name="grouping" type="select" optional="false" multiple="true" label="Browse group to compare"> | |
| 311 <option value="condition" selected="true">condition</option> | |
| 312 <option value="timepoint" selected="true">timepoint</option> | |
| 313 </param> | |
| 314 </xml> | |
| 315 <xml name="correction_method"> | |
| 316 <param name="correction_method" type="select" value="bonferroni" display="radio" label="Select multiple test correction to apply" help="Please enter at max 1 method"> | |
| 317 <option value="bonferroni">bonferroni</option> | |
| 318 <option value="holm-sidak">holm-sidak</option> | |
| 319 <option value="holm">holm</option> | |
| 320 <option value="simes-hochberg">simes-hochberg</option> | |
| 321 <option value="hommel">hommel</option> | |
| 322 <option value="fdr_bh">fdr_bh</option> | |
| 323 <option value="fdr_by">fdr_by</option> | |
| 324 <option value="fdr_tsbh">fdr_tsbh</option> | |
| 325 <option value="fdr_tsbky">fdr_tsbky</option> | |
| 326 </param> | |
| 327 </xml> | |
| 328 <xml name="compartments_enrichment"> | |
| 329 <param name="compartments" type="select" optional="false" multiple="true" | |
| 330 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> | |
| 331 <options from_dataset="metadata_path"> | |
| 332 <column name="compartment" index="4"/> | |
| 333 <column name="value" index="4"/> | |
| 334 <filter type="unique_value" name="compartment" column="4"/> | |
| 335 <filter type="remove_value" value="compartment"/> | |
| 336 </options> | |
| 337 <sanitizer> | |
| 338 <valid initial="default"> | |
| 339 <add preset="string.printable"/> | |
| 340 <add value="\t"/> | |
| 341 <remove value="""/> | |
| 342 <remove value="'"/> | |
| 343 </valid> | |
| 344 </sanitizer> | |
| 345 </param> | |
| 346 </xml> | |
| 347 <xml name="compartments_abundance"> | |
| 348 <param name="compartments" type="select" optional="false" multiple="true" | |
| 349 label="Browse compartments from metadata file (All needed). You have to load a metadata file prior to have access to compartments"> | |
| 350 <options from_dataset="metadata_path"> | |
| 351 <column name="compartment" index="4"/> | |
| 352 <column name="value" index="4"/> | |
| 353 <filter type="unique_value" name="compartment" column="4"/> | |
| 354 <filter type="remove_value" value="compartment"/> | |
| 355 </options> | |
| 356 <sanitizer> | |
| 357 <valid initial="default"> | |
| 358 <add preset="string.printable"/> | |
| 359 <add value="\t"/> | |
| 360 <remove value="""/> | |
| 361 <remove value="'"/> | |
| 362 </valid> | |
| 363 </sanitizer> | |
| 364 </param> | |
| 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="""/> | |
| 380 <remove value="'"/> | |
| 381 </valid> | |
| 382 </sanitizer> | |
| 383 </param> | |
| 384 </xml> | |
| 385 <xml name="compartments"> | |
| 386 <param name="compartments" type="select" optional="false" multiple="true" | |
| 387 label="Browse compartments from metadata file (1 min.). You have to load a metadata file prior to have access to compartments"> | |
| 388 <options from_dataset="metadata_path"> | |
| 389 <column name="compartment" index="4"/> | |
| 390 <column name="value" index="4"/> | |
| 391 <filter type="unique_value" name="compartment" column="4"/> | |
| 392 <filter type="remove_value" value="compartment"/> | |
| 393 </options> | |
| 394 <sanitizer> | |
| 395 <valid initial="default"> | |
| 396 <add preset="string.printable"/> | |
| 397 <add value="\t"/> | |
| 398 <remove value="""/> | |
| 399 <remove value="'"/> | |
| 400 </valid> | |
| 401 </sanitizer> | |
| 402 </param> | |
| 403 </xml> | |
| 404 <xml name="abundance_metabolites_list"> | |
| 405 <param name="metabolites_list" type="select" optional="false" multiple="true" | |
| 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"> | |
| 407 <validator type="length" min="1" message="Please enter at max 2 compartments"/> | |
| 408 <options from_dataset="abundance_file"> | |
| 409 <column name="metabolite_or_isotopologue" index="0"/> | |
| 410 <column name="value" index="0"/> | |
| 411 <filter type="unique_value" name="metabolite_or_isotopologue" column="0"/> | |
| 412 <filter type="remove_value" value="metabolite_or_isotopologue"/> | |
| 413 </options> | |
| 414 <sanitizer> | |
| 415 <valid initial="default"> | |
| 416 <add preset="string.printable"/> | |
| 417 <add value="\t"/> | |
| 418 <remove value="""/> | |
| 419 <remove value="'"/> | |
| 420 </valid> | |
| 421 </sanitizer> | |
| 422 </param> | |
| 423 </xml> | |
| 424 <xml name="enrichment_metabolites_list"> | |
| 425 <param name="metabolites_list" type="select" optional="false" multiple="true" | |
| 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"> | |
| 427 <validator type="length" min="1" message="Please enter at min 1 metabolite"/> | |
| 428 <options from_dataset="me_or_frac_contrib_file"> | |
| 429 <column name="ID" index="0"/> | |
| 430 <column name="value" index="0"/> | |
| 431 <filter type="unique_value" name="ID" column="0"/> | |
| 432 <filter type="remove_value" value="ID"/> | |
| 433 </options> | |
| 434 <sanitizer> | |
| 435 <valid initial="default"> | |
| 436 <add preset="string.printable"/> | |
| 437 <add value="\t"/> | |
| 438 <remove value="""/> | |
| 439 <remove value="'"/> | |
| 440 </valid> | |
| 441 </sanitizer> | |
| 442 </param> | |
| 443 </xml> | |
| 444 <xml name="isotopologue_metabolites_list"> | |
| 445 <param name="metabolites_list" type="select" optional="false" multiple="true" | |
| 446 label="Select Metabolite(s) to plot (1 Min.). You have to load a abundance file prior to have access to metabolite list"> | |
| 447 <validator type="length" min="1" message="Please enter at min 1 metabolite"/> | |
| 448 <options from_dataset="isotop_prop_file"> | |
| 449 <column name="ID" index="0"/> | |
| 450 <column name="value" index="0"/> | |
| 451 <filter type="unique_value" name="ID" column="0"/> | |
| 452 <filter type="remove_value" value="ID"/> | |
| 453 </options> | |
| 454 <sanitizer> | |
| 455 <valid initial="default"> | |
| 456 <add preset="string.printable"/> | |
| 457 <add value="\t"/> | |
| 458 <remove value="""/> | |
| 459 <remove value="'"/> | |
| 460 </valid> | |
| 461 </sanitizer> | |
| 462 </param> | |
| 463 </xml> | |
| 464 <xml name="deg_list"> | |
| 465 <repeat name="deg_list" title="Deregulated gene set" default="1" min="1"> | |
| 466 <param name="input" type="data" format="tabular" label="Deregulated genes set"/> | |
| 467 <param name="idcol" type="data_column" data_ref="input" label="Column for id" 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="""/> | |
| 482 <remove value="'"/> | |
| 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="""/> | |
| 499 <remove value="'"/> | |
| 500 </valid> | |
| 501 </sanitizer> | |
| 502 </param> | |
| 503 </repeat> | |
| 504 | |
| 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="""/> | |
| 521 <remove value="'"/> | |
| 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="""/> | |
| 541 <remove value="'"/> | |
| 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="""/> | |
| 561 <remove value="'"/> | |
| 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> | |
| 576 </xml> | |
| 577 <token name="@INIT_PCA@"><![CDATA[ | |
| 578 #import json | |
| 579 #import re | |
| 580 | |
| 581 mkdir -p data && | |
| 582 | |
| 583 #if $metadata_path: | |
| 584 ln -s '$metadata_path' data/metadata.csv && | |
| 585 #end if | |
| 586 #if $abundance_file: | |
| 587 ln -s '$abundance_file' data/abundance.csv && | |
| 588 #end if | |
| 589 #if $me_or_frac_contrib_file: | |
| 590 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && | |
| 591 #end if | |
| 592 | |
| 593 ]]></token> | |
| 594 <token name="@INIT_CONFIG@"><![CDATA[ | |
| 595 mkdir -p '$__new_file_path__/config' && | |
| 596 touch '$__new_file_path__/config/config.yaml' && | |
| 597 ]]></token> | |
| 598 <token name="@REMOVE_CONFIG@"><![CDATA[ | |
| 599 && rm -r '$__new_file_path__/config' | |
| 600 ]]></token> | |
| 601 <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[ | |
| 602 | |
| 603 mkdir -p data && | |
| 604 | |
| 605 #if $metadata_path: | |
| 606 ln -s '$metadata_path' data/metadata.csv && | |
| 607 #end if | |
| 608 #if $abundance_file: | |
| 609 ln -s '$abundance_file' data/abundance.csv && | |
| 610 #end if | |
| 611 ]]></token> | |
| 612 <token name="@INIT_ENRICHMENT_PLOT@"><![CDATA[ | |
| 613 | |
| 614 mkdir -p data && | |
| 615 | |
| 616 #if $metadata_path: | |
| 617 ln -s '$metadata_path' data/metadata.csv && | |
| 618 #end if | |
| 619 #if $me_or_frac_contrib_file: | |
| 620 ln -s '$me_or_frac_contrib_file' data/me_or_frac_contrib.csv && | |
| 621 #end if | |
| 622 ]]></token> | |
| 623 <token name="@INIT_ISOTOPOLOGUE_PLOT@"><![CDATA[ | |
| 624 | |
| 625 mkdir -p data && | |
| 626 | |
| 627 #if $metadata_path: | |
| 628 ln -s '$metadata_path' data/metadata.csv && | |
| 629 #end if | |
| 630 #if $isotop_prop_file: | |
| 631 ln -s '$isotop_prop_file' data/isotop_prop.csv && | |
| 632 #end if | |
| 633 ]]></token> | |
| 634 <token name="@INIT_BI_ANALYSIS@"><![CDATA[ | |
| 635 | |
| 636 mkdir -p data && | |
| 637 | |
| 638 #if $metadata_path: | |
| 639 ln -s '$metadata_path' data/metadata.csv && | |
| 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' | |
| 648 | |
| 649 #set $impute_values = {} | |
| 650 #if str( $data_input.data_input_selector ) == "abundance": | |
| 651 #if $data_input.abundance_file: | |
| 652 ln -s '$data_input.abundance_file' data/abundance.csv && | |
| 653 #silent $impute_values['abundances']='min' | |
| 654 #end if | |
| 655 #elif str( $data_input.data_input_selector ) == "mean_enrichment": | |
| 656 #if $data_input.me_or_frac_contrib_file: | |
| 657 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && | |
| 658 #silent $impute_values['mean_enrichment']='min' | |
| 659 #end if | |
| 660 #elif str( $data_input.data_input_selector ) == "isotop_prop": | |
| 661 #if $data_input.isotop_prop_file: | |
| 662 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && | |
| 663 #silent $impute_values['isotopologue_proportions']='min' | |
| 664 #end if | |
| 665 #else | |
| 666 #if $data_input.isotop_abs_file: | |
| 667 ln -s '$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 && | |
| 699 #silent $impute_values['isotopologues']='min' | |
| 700 #end if | |
| 701 #end if | |
| 702 ]]></token> | |
| 703 <token name="@INIT_METABOLOGRAM@"><![CDATA[ | |
| 704 #import json | |
| 705 #import re | |
| 706 #import os | |
| 707 #import csv | |
| 708 #import subprocess | |
| 709 | |
| 710 mkdir -p data && | |
| 711 | |
| 712 #if $path_kegg_metabolites: | |
| 713 ln -s '$path_kegg_metabolites' data/pathways_kegg_metabolites.csv && | |
| 714 #end if | |
| 715 #if $path_kegg_transcripts: | |
| 716 ln -s '$path_kegg_transcripts' data/pathways_kegg_transcripts.csv && | |
| 717 #end if | |
| 718 | |
| 719 #if $metadata_path: | |
| 720 ln -s '$metadata_path' data/metadata.csv && | |
| 721 #end if | |
| 722 | |
| 723 #set $impute_values = {} | |
| 724 #if str( $data_input.data_input_selector ) == "abundance": | |
| 725 #if $data_input.abundance_file: | |
| 726 ln -s '$data_input.abundance_file' data/abundance.csv && | |
| 727 #silent $impute_values['abundances']='min' | |
| 728 #end if | |
| 729 #else: | |
| 730 #if $data_input.me_or_frac_contrib_file: | |
| 731 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && | |
| 732 #silent $impute_values['mean_enrichment']='min' | |
| 733 #end if | |
| 734 #end if | |
| 735 | |
| 736 #for $i, $s in enumerate($deg_list) | |
| 737 #set $cpt = str($i+1) | |
| 738 ln -s '${s.input}' data/DEG_comparison'${cpt}'.csv && | |
| 739 #end for | |
| 740 | |
| 741 | |
| 742 ]]></token> | |
| 743 <token name="@INIT_DIFF_MULTIGROUP_ANALYSIS@"><![CDATA[ | |
| 744 | |
| 745 mkdir -p data && | |
| 746 | |
| 747 #if $metadata_path: | |
| 748 ln -s '$metadata_path' data/metadata.csv && | |
| 749 #end if | |
| 750 | |
| 751 #set $impute_values = {} | |
| 752 #if str( $data_input.data_input_selector ) == "abundance": | |
| 753 #if $data_input.abundance_file: | |
| 754 ln -s '$data_input.abundance_file' data/abundance.csv && | |
| 755 #silent $impute_values['abundances']='min' | |
| 756 #end if | |
| 757 #elif str( $data_input.data_input_selector ) == "mean_enrichment": | |
| 758 #if $data_input.me_or_frac_contrib_file: | |
| 759 ln -s '$data_input.me_or_frac_contrib_file' data/me_or_frac_contrib.csv && | |
| 760 #silent $impute_values['mean_enrichment']='min' | |
| 761 #end if | |
| 762 #elif str( $data_input.data_input_selector ) == "isotop_prop": | |
| 763 #if $data_input.isotop_prop_file: | |
| 764 ln -s '$data_input.isotop_prop_file' data/isotop_prop.csv && | |
| 765 #silent $impute_values['isotopologue_proportions']='min' | |
| 766 #end if | |
| 767 #else | |
| 768 #if $data_input.isotop_abs_file: | |
| 769 ln -s '$data_input.isotop_abs_file' data/isotop_abs.csv && | |
| 770 #silent $impute_values['isotopologues']='min' | |
| 771 #end if | |
| 772 #end if | |
| 773 ]]></token> | |
| 774 <token name="@INIT_IMPUTE_VALUES@"><![CDATA[ | |
| 775 #import re | |
| 776 #set $impute_values = {} | |
| 777 #if $abundance_file: | |
| 778 #silent $impute_values['abundances']='min' | |
| 779 #end if | |
| 780 #if $me_or_frac_contrib_file: | |
| 781 #silent $impute_values['mean_enrichment']='min' | |
| 782 #end if | |
| 783 ]]></token> | |
| 784 <token name="@INIT_DATATYPES@"><![CDATA[ | |
| 785 #import re | |
| 786 #set $datatypes_avail = list() | |
| 787 #if str( $data_input.data_input_selector ) == "abundance": | |
| 788 #if $data_input.abundance_file: | |
| 789 $datatypes_avail.append(re.sub('"', '', "abundances")) | |
| 790 #end if | |
| 791 #elif str( $data_input.data_input_selector ) == "mean_enrichment": | |
| 792 #if $data_input.me_or_frac_contrib_file: | |
| 793 $datatypes_avail.append(re.sub('"', '', "mean_enrichment")) | |
| 794 #end if | |
| 795 #elif str( $data_input.data_input_selector ) == "isotop_prop": | |
| 796 #if $data_input.isotop_prop_file: | |
| 797 $datatypes_avail.append(re.sub('"', '', "isotopologue_proportions")) | |
| 798 #end if | |
| 799 #else | |
| 800 #if $data_input.isotop_abs_file: | |
| 801 $datatypes_avail.append(re.sub('"', '', "isotopologues")) | |
| 802 #end if | |
| 803 #end if | |
| 804 ]]></token> | |
| 805 <token name="@INIT_STAT_TEST@"><![CDATA[ | |
| 806 #import re | |
| 807 #set $statistical_test = {} | |
| 808 #if str( $data_input.data_input_selector ) == "abundance": | |
| 809 #if $data_input.abundance_file: | |
| 810 #silent $statistical_test['abundances']=str($data_input.stat_test) | |
| 811 #end if | |
| 812 #elif str( $data_input.data_input_selector ) == "mean_enrichment": | |
| 813 #if $data_input.me_or_frac_contrib_file: | |
| 814 #silent $statistical_test['mean_enrichment']=str($data_input.stat_test) | |
| 815 #end if | |
| 816 #elif str( $data_input.data_input_selector ) == "isotop_prop": | |
| 817 #if $data_input.isotop_prop_file: | |
| 818 #silent $statistical_test['isotopologue_proportions']=str($data_input.stat_test) | |
| 819 #end if | |
| 820 #else | |
| 821 #if $data_input.isotop_abs_file: | |
| 822 #silent $statistical_test['isotopologues']=str($data_input.stat_test) | |
| 823 #end if | |
| 824 #end if | |
| 825 ]]></token> | |
| 826 <token name="@INIT_CONDITIONS@"><![CDATA[ | |
| 827 #import re | |
| 828 #set $conds = list() | |
| 829 #for $co in $conditions: | |
| 830 $conds.append(re.sub('"', '', str($co))) | |
| 831 #end for | |
| 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> | |
| 847 <token name="@INIT_TIMEPOINTS@"><![CDATA[ | |
| 848 | |
| 849 #import re | |
| 850 #set $timepoints = list() | |
| 851 #for $tp in $timepoint: | |
| 852 $timepoints.append(re.sub('"', '', str($tp))) | |
| 853 #end for | |
| 854 ]]></token> | |
| 855 <token name="@INIT_GROUPS@"><![CDATA[ | |
| 856 #import re | |
| 857 #set $groups = list() | |
| 858 $groups.append(re.sub('"', '', str("condition"))) | |
| 859 $groups.append(re.sub('"', '', str("timepoint"))) | |
| 860 | |
| 861 ]]></token> | |
| 862 <token name="@INIT_ENRICHMENT_METABOLITES@"><![CDATA[ | |
| 863 #import json | |
| 864 #import re | |
| 865 #set $metabolites = {} | |
| 866 #for $cp in $compartments: | |
| 867 #silent $metabolites[re.sub('"', '', str($cp))]=list() | |
| 868 #for $met in $metabolites_list: | |
| 869 #set tmp_met=re.sub('\,', '%%',str($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))) | |
| 873 #end for | |
| 874 #end for | |
| 875 ]]></token> | |
| 876 <token name="@INIT_ISOTOPOLOGUE_METABOLITES@"><![CDATA[ | |
| 877 #set $metabolites = {} | |
| 878 #for $cp in $compartments: | |
| 879 #silent $metabolites[re.sub('"', '', str($cp))]=list() | |
| 880 #for $met in $metabolites_list: | |
| 881 #set tmp_met=re.sub('\,', '--',str($met)) | |
| 882 #set tmp_met_bis=str(re.split('_m', str($tmp_met))[0]) | |
| 883 #set tmp_met_ter=re.sub('--', '\,',str($tmp_met_bis)) | |
| 884 $metabolites[re.sub('"', '', str($cp))].append(re.sub('"', '\'', str(tmp_met_ter))) | |
| 885 #end for | |
| 886 #end for | |
| 887 ]]></token> | |
| 888 <token name="@INIT_MULTIGROUP_COMPARISONS@"><![CDATA[ | |
| 889 #set $comparisons = list() | |
| 890 #for $tp in $timepoint: | |
| 891 #set $ctrl_found=False | |
| 892 #set $ctrl="" | |
| 893 | |
| 894 #for $co in $conditions: | |
| 895 #set $sub_comparisons = list() | |
| 896 #if str($co) in ["Control", "control","ctrl"]: | |
| 897 #set $ctrl_found=True | |
| 898 #set $ctrl=str($co) | |
| 899 $sub_comparisons.append(re.sub('"', '', str($co))) | |
| 900 $sub_comparisons.append(re.sub('"', '', str($tp))) | |
| 901 #else: | |
| 902 $sub_comparisons.append(re.sub('"', '', str($co))) | |
| 903 $sub_comparisons.append(re.sub('"', '', str($tp))) | |
| 904 | |
| 905 #end if | |
| 906 $comparisons.append($sub_comparisons) | |
| 907 #end for | |
| 908 #end for | |
| 909 ]]></token> | |
| 910 <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[ | |
| 911 #import re | |
| 912 #set $conditions = list() | |
| 913 #for $i, $s in enumerate($factor_list) | |
| 914 #set $cpt = str($i+1) | |
| 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 | |
| 949 | |
| 950 ]]></token> | |
| 951 <token name="@INIT_COMPARISONS@"><![CDATA[ | |
| 952 #import re | |
| 953 #set $conds = list() | |
| 954 #for $co in $conditions: | |
| 955 $conds.append(re.sub('"', '', str($co))) | |
| 956 #end for | |
| 957 #set $timepoints = list() | |
| 958 #for $tp in $timepoint: | |
| 959 $timepoints.append(re.sub('"', '', str($tp))) | |
| 960 #end for | |
| 961 | |
| 962 #set $comparisons = list() | |
| 963 #if len($conds) > 1: | |
| 964 #if len($timepoints) > 0: | |
| 965 #for $tp in $timepoint: | |
| 966 #set $ctrl_found=False | |
| 967 #set $ctrl="" | |
| 968 #set $comparisons_bis = list() | |
| 969 #for $co in $conditions: | |
| 970 #set $sub_comparisons = list() | |
| 971 #if str($co) in ["'Control'", "'control'", "'ctrl'"]: | |
| 972 #set $ctrl_found=True | |
| 973 #set $ctrl=str($co) | |
| 974 #else: | |
| 975 $sub_comparisons.append(re.sub('"', '', str($co))) | |
| 976 $sub_comparisons.append(re.sub('"', '', str($tp))) | |
| 977 | |
| 978 #end if | |
| 979 $comparisons_bis.append($sub_comparisons) | |
| 980 #end for | |
| 981 | |
| 982 #if $ctrl_found: | |
| 983 $sub_comparisons.append(str($ctrl)) | |
| 984 $sub_comparisons.append(str($tp)) | |
| 985 $comparisons_bis.append($sub_comparisons) | |
| 986 #end if | |
| 987 | |
| 988 $comparisons.append($comparisons_bis) | |
| 989 #end for | |
| 990 #else | |
| 991 #for $co in $conditions: | |
| 992 $comparisons.append(re.sub('"', '', str($co))) | |
| 993 #end for | |
| 994 #end if | |
| 995 | |
| 996 #else | |
| 997 #if len($conds) > 0: | |
| 998 #if len($timepoints) > 1: | |
| 999 #for $co in $conditions: | |
| 1000 #set $comparisons_bis = list() | |
| 1001 #for $tp in $timepoint: | |
| 1002 #set $sub_comparisons = list() | |
| 1003 $sub_comparisons.append(re.sub('"', '', str($co))) | |
| 1004 $sub_comparisons.append(re.sub('"', '', str($tp))) | |
| 1005 $comparisons_bis.append($sub_comparisons) | |
| 1006 #end for | |
| 1007 $comparisons.append($comparisons_bis) | |
| 1008 #end for | |
| 1009 #end if | |
| 1010 #else | |
| 1011 #for $tp in $timepoint: | |
| 1012 $comparisons.append(re.sub('"', '', str($tp))) | |
| 1013 #end for | |
| 1014 #end if | |
| 1015 #end if | |
| 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> | |
| 1086 <token name="@INIT_TRANSCRIPTS@"><![CDATA[ | |
| 1087 #import re | |
| 1088 #import os | |
| 1089 #import subprocess | |
| 1090 #set $transcripts = list() | |
| 1091 | |
| 1092 #for $i, $s in enumerate($deg_list) | |
| 1093 #set $cpt = str($i+1) | |
| 1094 $transcripts.append(re.sub('"', '', "DEG_comparison"+str($i+1))) | |
| 1095 #set $deg_one_values = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.valuecol), shell=True)) | |
| 1096 #set $deg_one_id = os.fsdecode(subprocess.check_output('head -n1 ' + str($s.input) + '| cut -f' + str($s.idcol), shell=True)) | |
| 1097 #end for | |
| 1098 ]]></token> | |
| 1099 <token name="@INIT_PATHWAYS@"><![CDATA[ | |
| 1100 #set $pathways = {} | |
| 1101 #if $path_kegg_metabolites: | |
| 1102 #silent $pathways['metabolites']='pathways_kegg_metabolites' | |
| 1103 #end if | |
| 1104 #if $path_kegg_transcripts: | |
| 1105 #silent $pathways['transcripts']='pathways_kegg_transcripts' | |
| 1106 #end if | |
| 1107 ]]></token> | |
| 1108 </macros> |