Mercurial > repos > iuc > raceid_inspecttrajectory
comparison macros_cheetah.xml @ 6:c8434a623268 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author | iuc |
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date | Thu, 15 Apr 2021 18:58:58 +0000 |
parents | 86e2358cf273 |
children | a6821f856a1e |
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5:69018f285aa3 | 6:c8434a623268 |
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125 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' ) | 125 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' ) |
126 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' ) | 126 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' ) |
127 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' ) | 127 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' ) |
128 #end if | 128 #end if |
129 | 129 |
130 cluster.compumap = formals(compumap) | |
130 cluster.comptsne = formals(comptsne) | 131 cluster.comptsne = formals(comptsne) |
131 cluster.compfr = formals(compfr) | 132 cluster.compfr = formals(compfr) |
132 | 133 |
133 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' ) | 134 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' ) |
134 cluster.compfr\$knn = as.integer( '$tsne.knn' ) | 135 cluster.compfr\$knn = as.integer( '$tsne.knn' ) |
136 cluster.compumap\$n_neighbors = as.integer( '$tsne.umap_nn' ) | |
135 #if str($tsne.use.def) == "no": | 137 #if str($tsne.use.def) == "no": |
136 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' ) | 138 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' ) |
137 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' ) | 139 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' ) |
138 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' ) | 140 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' ) |
141 cluster.compumap\$n_epochs = as.integer( '$tsne.use.umap_epochs' ) | |
142 cluster.compumap\$min_dist = as.numeric( '$tsne.use.umap_min_dist' ) | |
139 #end if | 143 #end if |
140 | 144 |
141 genelist.tablelim = as.integer( '$extra.tablelim' ) | 145 genelist.tablelim = as.integer( '$extra.tablelim' ) |
142 genelist.plotlim = as.integer( '$extra.plotlim' ) | 146 genelist.plotlim = as.integer( '$extra.plotlim' ) |
143 genelist.foldchange = as.integer( '$extra.foldchange' ) | 147 genelist.foldchange = as.integer( '$extra.foldchange' ) |
225 plotdiffg = formals(plotdiffgenesnb) | 229 plotdiffg = formals(plotdiffgenesnb) |
226 | 230 |
227 perform.diffgene = TRUE | 231 perform.diffgene = TRUE |
228 plotdiffg\$Aname = '$diffgtest.set_a.name_set' | 232 plotdiffg\$Aname = '$diffgtest.set_a.name_set' |
229 plotdiffg\$Bname = '$diffgtest.set_b.name_set' | 233 plotdiffg\$Bname = '$diffgtest.set_b.name_set' |
234 plotdiffg\$... = NULL | |
230 | 235 |
231 gfdat.A.use = list() | 236 gfdat.A.use = list() |
232 gfdat.B.use = list() | 237 gfdat.B.use = list() |
233 | 238 |
234 gfdat.A.use\$manual = NULL | 239 gfdat.A.use\$manual = NULL |
292 | 297 |
293 pstc.plotgraph = formals(plotgraph) | 298 pstc.plotgraph = formals(plotgraph) |
294 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' ) | 299 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' ) |
295 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' ) | 300 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' ) |
296 #if str($plotgraph.use.def) == "no": | 301 #if str($plotgraph.use.def) == "no": |
297 pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) | 302 ##pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' ) |
298 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' ) | 303 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' ) |
299 #end if | 304 #end if |
300 | 305 |
301 pstc.compscore = formals(compscore) | 306 pstc.compscore = formals(compscore) |
302 pstc.compscore\$nn = as.integer( '$compscore.nn' ) | 307 pstc.compscore\$nn = as.integer( '$compscore.nn' ) |