Mercurial > repos > iuc > raceid_inspectclusters

comparison macros_cheetah.xml @ 6:41f34e925bd5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 18:59:31 +0000
parents 20f522154663
children f3eb2291da05
comparison
equal deleted inserted replaced
5:37a47c4fd84d 6:41f34e925bd5
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' )