Mercurial > repos > iuc > raceid_clustering

comparison macros_cheetah.xml @ 4:ee0bbc160cb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 13:00:12 -0400
parents
children a4b734cd253b
comparison
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3:d4646ce659b4 4:ee0bbc160cb1
1 <macros>
2 <token name="@FILTNORM_CHEETAH@"><![CDATA[
3 ## Perform do.filter
4 use.filtnormconf = TRUE
5
6 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
7 use.cluster = FALSE
8
9 in.table = read.table(
10 '${intable}',
11 stringsAsFactors = F,
12 na.strings=c("NA", "-", "?", "."),
13 sep='\t',
14 header=TRUE,
15 row.names=1
16 )
17
18 ## Hidden flag to use test data instead
19 ## see: test-data/use.intestinal
20
21 use.test.data = (names(in.table)[1] == "test")
22
23 sc = NULL
24 if (use.test.data) {
25 sc = SCseq(intestinalData)
26 message("Loading test data from library")
27 } else {
28 sc = SCseq(in.table)
29 }
30
31
32 filt = formals(filterdata)
33 filt.ccc = formals(CCcorrect)
34 filt.use.ccorrect = FALSE
35 filt.lbatch.regexes = NULL
36
37 filt.geqone = as.logical( '$filt.hist_geq_one' )
38 filt\$mintotal = as.integer( '$filt.mintotal' )
39 filt\$minexpr = as.integer( '$filt.minexpr' )
40 filt\$minnumber = as.integer( '$filt.minnumber' )
41 #if str($filt.use.def) == "no":
42 filt\$knn = as.integer( '$filt.use.knn' )
43 filt\$ccor = as.numeric( '$filt.use.ccor' )
44 filt\$bmode = as.character( '$filt.use.bmode' )
45 #if $filt.use.LBatch_regexes:
46 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
47 #end if
48 #if $filt.use.CGenes:
49 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
50 #end if
51 #if $filt.use.FGenes:
52 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
53 #end if
54 #if str($filt.use.ccc.use) == "yes"
55 filt.use.ccorrect = TRUE
56 #if $filt.use.ccc.vset:
57 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
58 #end if
59 #if $filt.use.ccc.ncomp:
60 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
61 #end if
62 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
63 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
64 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
65 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
66 filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
67 #end if
68 #end if
69
70 out.pdf = '${outpdf}'
71 out.rdat = '${outrdat}'
72 out.table = '${outtable}'
73
74 ]]></token>
75 <token name="@CLUSTER_CHEETAH@"><![CDATA[
76
77 in.rdat = readRDS('${inputrds}')
78
79 sc = in.rdat
80
81 ## Perform do.filter
82 use.filtnormconf = FALSE
83
84 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
85 use.cluster = TRUE
86
87
88 clust.compdist = formals(compdist)
89 clust.clustexp = formals(clustexp)
90 clust.compdist\$metric = as.character( '$clust.metric' )
91 clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
92
93 #if str($clust.use.def) == "no":
94
95 clust.compdist\$FSelect = as.logical( '$clust.use.fselect' )
96 #if $clust.use.knn:
97 clust.compdist\$knn = as.integer( '$clust.use.knn' )
98 #end if
99 clust.clustexp\$sat = as.logical( '$clust.use.sat' )
100 #if $clust.use.samp:
101 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
102 #end if
103 #if $clust.use.cln:
104 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
105 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
107 ##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
108 #end if
109 #end if
110
111 outlier.use.randomforest = FALSE
112 outlier.findoutliers = formals(findoutliers)
113 outlier.clustheatmap = formals(clustheatmap)
114 outlier.rfcorrect = formals(rfcorrect)
115
116 outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
117 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
118 outlier.rfcorrect\$final = as.logical( '$outlier.final' )
119
120 #if str($outlier.use.def) == "no":
121 #if $outlier.use.nbtree:
122 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
123 #end if
124 outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
125 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
126 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
127 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
128 #end if
129
130 cluster.comptsne = formals(comptsne)
131 cluster.compfr = formals(compfr)
132
133 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
134 cluster.compfr\$knn = as.integer( '$tsne.knn' )
135 #if str($tsne.use.def) == "no":
136 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
137 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
138 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
139 #end if
140
141 genelist.tablelim = as.integer( '$extra.tablelim' )
142 genelist.plotlim = as.integer( '$extra.plotlim' )
143 genelist.foldchange = as.integer( '$extra.foldchange' )
144 genelist.pvalue = as.numeric( '$extra.pvalue' )
145
146 out.pdf = '${outpdf}'
147 out.rdat = '${outrdat}'
148 out.genelist = '${outgenelist}'
149 out.assignments = '${outassignments}'
150 out.log = '${outlog}'
151
152 ]]>
153 </token>
154 <token name="@INSPECTCLUSTERS_CHEETAH@"><![CDATA[
155 in.rdat = readRDS('${inputrds}')
156
157 perform.plotting = FALSE
158 perform.symbolmap = FALSE
159 perform.genesofinterest = FALSE
160 perform.diffgene = FALSE
161
162 #if str($plotgen.do_opt) == "yes":
163 perform.plotting = TRUE
164 plotting.cln = string2numericvector( '$plotgen.clusts_plot' )
165 #end if
166
167 #if str($plotsym.do_opt) == "yes":
168 perform.symbolmap = TRUE
169 plotsym = formals(plotsymbolsmap)
170 plotsym.use.typeremoveregex = NULL
171 plotsym.use.typeremoveregex.subselect = NULL
172 plotsym.use.typeremoveregex = as.character( '$plotsym.types_regex' )
173 #if str($plotsym.use.def) == "no":
174 plotsym\$fr = as.logical( '$plotsym.use.fr' )
175 #if $plotsym.use.subset_regex:
176 plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
177 #end if
178 #end if
179 #end if
180
181 #if str($gois.do_opt) == "yes":
182 perform.genesofinterest = TRUE
183 plotexp = formals(plotexpmap)
184 plotmarkg = formals(plotmarkergenes)
185
186 inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
187 plotexp\$g = inspect.goi.use.genes
188 plotmarkg\$genes = inspect.goi.use.genes
189
190 #if $gois.inspect_goi_cells:
191 inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
192 plotexp\$cells = inspect.goi.use.cells
193 plotmarkg\$cells = inspect.goi.use.cells
194 #end if
195 #if str($gois.use.def) == "no":
196 inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
197 plotexp\$imputed = inspect.goi.use.imputed
198 plotmarkg\$imputed = inspect.goi.use.imputed
199 #if $gois.use.plotmarkg_cl
200 plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
201 #end if
202 #if $gois.use.plotmarkg_cap
203 plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
204 #end if
205 #if $gois.use.plotmarkg_flo
206 plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
207 #end if
208 #if $gois.use.plotmarkg_samples
209 plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
210 #end if
211 #if $gois.use.plotexp_n
212 plotexp\$n = as.character( '$gois.use.plotexp_n' )
213 #end if
214 plotmarkg\$cthr = as.integer( '$gois.use.plotmarkg_cthr' )
215 plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
216 plotmarkg\$aggr = as.logical( '$gois.use.plotmarkg_aggr' )
217 plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
218 plotmarkg\$cluster_cols = as.logical( '$gois.use.plotmarkg_cluster_cols' )
219 plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
220 plotmarkg\$cluster_set = as.logical( '$gois.use.plotmarkg_cluster_set' )
221 #end if
222 #end if
223
224 #if str($diffgtest.do_opt) == "yes":
225 plotdiffg = formals(plotdiffgenesnb)
226
227 perform.diffgene = TRUE
228 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
229 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
230
231 gfdat.A.use = list()
232 gfdat.B.use = list()
233
234 gfdat.A.use\$manual = NULL
235 gfdat.A.use\$regex = NULL
236 gfdat.A.use\$cln = NULL
237 gfdat.B.use\$manual = NULL
238 gfdat.B.use\$regex = NULL
239 gfdat.B.use\$cln = NULL
240
241 #if str($diffgtest.set_a.meth.type) == "cln":
242 gfdat.A.use\$cln = string2numericvector( '$diffgtest.set_a.meth.selector' )
243 #else if str($diffgtest.set_a.meth.type) == "regex":
244 gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
245 #else if str($diffgtest.set_a.meth.type) == "manual":
246 gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
247 #end if
248
249 #if str($diffgtest.set_b.meth.type) == "cln":
250 gfdat.B.use\$cln = string2numericvector( '$diffgtest.set_b.meth.selector' )
251 #else if str($diffgtest.set_b.meth.type) == "regex":
252 gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
253 #else if str($diffgtest.set_b.meth.type) == "manual":
254 gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
255 #end if
256
257 #if str($diffgtest.use.def) == "no":
258 plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
259 plotdiffg\$padj = as.logical( '$diffgtest.use.plotdiffg_padj' )
260 plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
261 plotdiffg\$show_names = as.logical( '$diffgtest.use.plotdiffg_show_names' )
262 #if $diffgtest.use.plotdiffg_mthr
263 plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
264 #end if
265 #end if
266 #end if
267
268 out.pdf='${outpdf}'
269 ]]></token>
270 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
271
272 in.rdat = readRDS('${inputrds}')
273
274 pstc.projc = formals(projcells)
275 pstc.projc\$knn = as.integer( '$projcell.knn' )
276 pstc.projc\$cthr = as.integer( '$projcell.cthr' )
277 #if str($projcell.use.def) == "no":
278 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
279 pstc.projc\$fr = as.logical( '$projcell.use.fr' )
280 #end if
281
282 pstc.projb = formals(projback)
283 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
284 #if str($projback.use.def) == "no":
285 pstc.projb\$fast = as.logical( '$projback.use.fast' )
286 pstc.projb\$rseed = as.integer( '$projback.use.rseed' )
287 #end if
288
289 pstc.comppval = formals(comppvalue)
290 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
291 pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' )
292
293 pstc.plotgraph = formals(plotgraph)
294 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
295 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
296 #if str($plotgraph.use.def) == "no":
297 pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
298 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
299 #end if
300
301 pstc.compscore = formals(compscore)
302 pstc.compscore\$nn = as.integer( '$compscore.nn' )
303 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
304
305 out.pdf='${outpdf}'
306 out.rdat='${outrdat}'
307 ]]></token>
308 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
309 in.rdat = readRDS('${inputrds}')
310
311 perform.stemID = FALSE
312 perform.fateID = FALSE
313 perform.fateID.sominspect = FALSE
314
315 #if str($trjsid.basic.doit) == "yes"
316 perform.stemID = TRUE
317 trjsid.getproj = formals(getproj)
318
319 trjsid.numdiffgenes = 10
320 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
321 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
322
323 #if str($trjsid.basic.use.def) == "no":
324
325 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
326 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
327
328 #end if
329 #end if
330
331 #if str($trjfid.basic.doit) == "yes":
332 perform.fateID = TRUE
333 trjfid.cellsfrom = formals(cellsfromtree)
334 trjfid.filterset = formals(filterset)
335 trjfid.getsom = formals(getsom)
336 trjfid.procsom = formals(procsom)
337 trjfid.plotheat = list()
338
339 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
340 #if str($trjfid.basic.use.def) == "no":
341
342 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
343 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
344 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
345 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
346 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
347 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
348 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
349 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
350 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
351 #end if
352
353 #if str($trjfid.basic.som.doit) == "yes":
354 perform.fateID.sominspect = TRUE
355
356 trjfidsomi = list()
357 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
358 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
359 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
360 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
361 #end if
362
363 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
364 trjfidsomi\$name = '$trjfid.basic.som.title'
365
366 #if str($trjfid.basic.som.use.def) == "no":
367 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
368 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
369 #end if
370 #end if
371 #end if
372
373 out.pdf = '${outpdf}'
374 out.diffgenes = '${outdiffgenes}'
375
376 ]]></token>
377 </macros>