Mercurial > repos > iuc > raceid_clustering

comparison macros_cheetah.xml @ 9:0bff0ee0683a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
author iuc
date Wed, 24 Aug 2022 18:09:06 +0000
parents a4b734cd253b
children
comparison
equal deleted inserted replaced
8:f911a64454fb 9:0bff0ee0683a
102 #end if 102 #end if
103 #if $clust.use.cln: 103 #if $clust.use.cln:
104 clust.clustexp\$cln = as.integer( '$clust.use.cln' ) 104 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
105 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' ) 105 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' ) 106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
107 ##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
108 #end if 107 #end if
109 #end if 108 #end if
110 109
111 outlier.use.randomforest = FALSE 110 outlier.use.randomforest = FALSE
112 outlier.findoutliers = formals(findoutliers) 111 outlier.findoutliers = formals(findoutliers)
311 out.rdat='${outrdat}' 310 out.rdat='${outrdat}'
312 ]]></token> 311 ]]></token>
313 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[ 312 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
314 in.rdat = readRDS('${inputrds}') 313 in.rdat = readRDS('${inputrds}')
315 314
316 perform.stemID = FALSE 315 perform.stemid = FALSE
317 perform.fateID = FALSE 316 perform.fateid = FALSE
318 perform.fateID.sominspect = FALSE 317 perform.fateid.sominspect = FALSE
319 318
320 #if str($trjsid.basic.doit) == "yes" 319 #if str($trjsid.basic.doit) == "yes"
321 perform.stemID = TRUE 320 perform.stemid = TRUE
322 trjsid.getproj = formals(getproj) 321 trjsid.getproj = formals(getproj)
323 322
324 trjsid.numdiffgenes = 10 323 trjsid.numdiffgenes = 10
325 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' ) 324 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
326 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' ) 325 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
332 331
333 #end if 332 #end if
334 #end if 333 #end if
335 334
336 #if str($trjfid.basic.doit) == "yes": 335 #if str($trjfid.basic.doit) == "yes":
337 perform.fateID = TRUE 336 perform.fateid = TRUE
338 trjfid.cellsfrom = formals(cellsfromtree) 337 trjfid_cellsfrom = formals(cellsfromtree)
339 trjfid.filterset = formals(filterset) 338 trjfid_filterset = formals(filterset)
340 trjfid.getsom = formals(getsom) 339 trjfid_getsom = formals(getsom)
341 trjfid.procsom = formals(procsom) 340 trjfid_procsom = formals(procsom)
342 trjfid.plotheat = list() 341 trjfid_plotheat = list()
343 342
344 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' ) 343 trjfid_cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
345 #if str($trjfid.basic.use.def) == "no": 344 #if str($trjfid.basic.use.def) == "no":
346 345
347 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' ) 346 trjfid_filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
348 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' ) 347 trjfid_filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
349 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' ) 348 trjfid_getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
350 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' ) 349 trjfid_getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
351 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' ) 350 trjfid_procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
352 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' ) 351 trjfid_procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
353 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' ) 352 trjfid_plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
354 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' ) 353 trjfid_plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
355 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' ) 354 trjfid_plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
356 #end if 355 #end if
357 356
358 #if str($trjfid.basic.som.doit) == "yes": 357 #if str($trjfid.basic.som.doit) == "yes":
359 perform.fateID.sominspect = TRUE 358 perform.fateid.sominspect = TRUE
360 359
361 trjfidsomi = list() 360 trjfidsomi = list()
362 #if str($trjfid.basic.som.use_genes.typer) == "genelist": 361 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
363 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' ) 362 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
364 #else if str($trjfid.basic.som.use_genes.typer) == "cln": 363 #else if str($trjfid.basic.som.use_genes.typer) == "cln":