Mercurial > repos > iuc > raceid_inspecttrajectory
comparison macros_cheetah.xml @ 4:86e2358cf273 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author | iuc |
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date | Mon, 12 Aug 2019 13:03:03 -0400 |
parents | |
children | c8434a623268 |
comparison
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3:4164c0da0a5d | 4:86e2358cf273 |
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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> |