raceid_inspecttrajectory: macros

annotate macros_cheetah.xml @ 9:a6821f856a1e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf

author	iuc
date	Wed, 24 Aug 2022 18:10:56 +0000
parents	c8434a623268
children

rev	line source
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	1 <macros>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	2 <token name="@FILTNORM_CHEETAH@"><![CDATA[
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	3 ## Perform do.filter
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	4 use.filtnormconf = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	5
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	6 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	7 use.cluster = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	8
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	9 in.table = read.table(
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	10 '${intable}',
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	11 stringsAsFactors = F,
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	12 na.strings=c("NA", "-", "?", "."),
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	13 sep='\t',
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	14 header=TRUE,
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	15 row.names=1
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	16 )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	17
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	18 ## Hidden flag to use test data instead
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	19 ## see: test-data/use.intestinal
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	20
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	21 use.test.data = (names(in.table)[1] == "test")
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	22
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	23 sc = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	24 if (use.test.data) {
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	25 sc = SCseq(intestinalData)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	26 message("Loading test data from library")
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	27 } else {
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	28 sc = SCseq(in.table)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	29 }
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	30
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	31
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	32 filt = formals(filterdata)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	33 filt.ccc = formals(CCcorrect)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	34 filt.use.ccorrect = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	35 filt.lbatch.regexes = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	36
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	37 filt.geqone = as.logical( '$filt.hist_geq_one' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	38 filt\$mintotal = as.integer( '$filt.mintotal' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	39 filt\$minexpr = as.integer( '$filt.minexpr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	40 filt\$minnumber = as.integer( '$filt.minnumber' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	41 #if str($filt.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	42 filt\$knn = as.integer( '$filt.use.knn' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	43 filt\$ccor = as.numeric( '$filt.use.ccor' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	44 filt\$bmode = as.character( '$filt.use.bmode' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	45 #if $filt.use.LBatch_regexes:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	46 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	47 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	48 #if $filt.use.CGenes:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	49 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	50 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	51 #if $filt.use.FGenes:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	52 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	53 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	54 #if str($filt.use.ccc.use) == "yes"
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	55 filt.use.ccorrect = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	56 #if $filt.use.ccc.vset:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	57 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	58 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	59 #if $filt.use.ccc.ncomp:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	60 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	61 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	62 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	63 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	64 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	65 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	66 filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	67 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	68 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	69
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	70 out.pdf = '${outpdf}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	71 out.rdat = '${outrdat}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	72 out.table = '${outtable}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	73
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	74 ]]></token>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	75 <token name="@CLUSTER_CHEETAH@"><![CDATA[
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	76
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	77 in.rdat = readRDS('${inputrds}')
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	78
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	79 sc = in.rdat
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	80
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	81 ## Perform do.filter
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	82 use.filtnormconf = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	83
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	84 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	85 use.cluster = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	86
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	87
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	88 clust.compdist = formals(compdist)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	89 clust.clustexp = formals(clustexp)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	90 clust.compdist\$metric = as.character( '$clust.metric' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	91 clust.clustexp\$FUNcluster = as.character( '$clust.funcluster' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	92
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	93 #if str($clust.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	94
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	95 clust.compdist\$FSelect = as.logical( '$clust.use.fselect' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	96 #if $clust.use.knn:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	97 clust.compdist\$knn = as.integer( '$clust.use.knn' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	98 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	99 clust.clustexp\$sat = as.logical( '$clust.use.sat' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	100 #if $clust.use.samp:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	101 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	102 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	103 #if $clust.use.cln:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	104 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	105 clust.clustexp\$clustnr = as.integer( '$clust.use.clustnr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	107 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	108 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	109
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	110 outlier.use.randomforest = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	111 outlier.findoutliers = formals(findoutliers)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	112 outlier.clustheatmap = formals(clustheatmap)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	113 outlier.rfcorrect = formals(rfcorrect)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	114
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	115 outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	116 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	117 outlier.rfcorrect\$final = as.logical( '$outlier.final' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	118
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	119 #if str($outlier.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	120 #if $outlier.use.nbtree:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	121 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	122 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	123 outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	124 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	125 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	126 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	127 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	128
6 c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	129 cluster.compumap = formals(compumap)
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	130 cluster.comptsne = formals(comptsne)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	131 cluster.compfr = formals(compfr)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	132
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	133 cluster.comptsne\$perplexity = as.integer( '$tsne.perplexity' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	134 cluster.compfr\$knn = as.integer( '$tsne.knn' )
6 c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	135 cluster.compumap\$n_neighbors = as.integer( '$tsne.umap_nn' )
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	136 #if str($tsne.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	137 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	138 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	139 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
6 c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	140 cluster.compumap\$n_epochs = as.integer( '$tsne.use.umap_epochs' )
c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	141 cluster.compumap\$min_dist = as.numeric( '$tsne.use.umap_min_dist' )
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	142 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	143
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	144 genelist.tablelim = as.integer( '$extra.tablelim' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	145 genelist.plotlim = as.integer( '$extra.plotlim' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	146 genelist.foldchange = as.integer( '$extra.foldchange' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	147 genelist.pvalue = as.numeric( '$extra.pvalue' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	148
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	149 out.pdf = '${outpdf}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	150 out.rdat = '${outrdat}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	151 out.genelist = '${outgenelist}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	152 out.assignments = '${outassignments}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	153 out.log = '${outlog}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	154
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	155 ]]>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	156 </token>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	157 <token name="@INSPECTCLUSTERS_CHEETAH@"><![CDATA[
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	158 in.rdat = readRDS('${inputrds}')
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	159
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	160 perform.plotting = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	161 perform.symbolmap = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	162 perform.genesofinterest = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	163 perform.diffgene = FALSE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	164
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	165 #if str($plotgen.do_opt) == "yes":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	166 perform.plotting = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	167 plotting.cln = string2numericvector( '$plotgen.clusts_plot' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	168 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	169
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	170 #if str($plotsym.do_opt) == "yes":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	171 perform.symbolmap = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	172 plotsym = formals(plotsymbolsmap)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	173 plotsym.use.typeremoveregex = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	174 plotsym.use.typeremoveregex.subselect = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	175 plotsym.use.typeremoveregex = as.character( '$plotsym.types_regex' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	176 #if str($plotsym.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	177 plotsym\$fr = as.logical( '$plotsym.use.fr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	178 #if $plotsym.use.subset_regex:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	179 plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	180 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	181 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	182 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	183
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	184 #if str($gois.do_opt) == "yes":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	185 perform.genesofinterest = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	186 plotexp = formals(plotexpmap)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	187 plotmarkg = formals(plotmarkergenes)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	188
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	189 inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	190 plotexp\$g = inspect.goi.use.genes
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	191 plotmarkg\$genes = inspect.goi.use.genes
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	192
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	193 #if $gois.inspect_goi_cells:
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	194 inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	195 plotexp\$cells = inspect.goi.use.cells
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	196 plotmarkg\$cells = inspect.goi.use.cells
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	197 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	198 #if str($gois.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	199 inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	200 plotexp\$imputed = inspect.goi.use.imputed
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	201 plotmarkg\$imputed = inspect.goi.use.imputed
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	202 #if $gois.use.plotmarkg_cl
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	203 plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	204 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	205 #if $gois.use.plotmarkg_cap
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	206 plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	207 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	208 #if $gois.use.plotmarkg_flo
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	209 plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	210 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	211 #if $gois.use.plotmarkg_samples
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	212 plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	213 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	214 #if $gois.use.plotexp_n
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	215 plotexp\$n = as.character( '$gois.use.plotexp_n' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	216 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	217 plotmarkg\$cthr = as.integer( '$gois.use.plotmarkg_cthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	218 plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	219 plotmarkg\$aggr = as.logical( '$gois.use.plotmarkg_aggr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	220 plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	221 plotmarkg\$cluster_cols = as.logical( '$gois.use.plotmarkg_cluster_cols' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	222 plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	223 plotmarkg\$cluster_set = as.logical( '$gois.use.plotmarkg_cluster_set' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	224 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	225 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	226
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	227 #if str($diffgtest.do_opt) == "yes":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	228 plotdiffg = formals(plotdiffgenesnb)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	229
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	230 perform.diffgene = TRUE
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	231 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	232 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
6 c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	233 plotdiffg\$... = NULL
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	234
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	235 gfdat.A.use = list()
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	236 gfdat.B.use = list()
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	237
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	238 gfdat.A.use\$manual = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	239 gfdat.A.use\$regex = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	240 gfdat.A.use\$cln = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	241 gfdat.B.use\$manual = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	242 gfdat.B.use\$regex = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	243 gfdat.B.use\$cln = NULL
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	244
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	245 #if str($diffgtest.set_a.meth.type) == "cln":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	246 gfdat.A.use\$cln = string2numericvector( '$diffgtest.set_a.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	247 #else if str($diffgtest.set_a.meth.type) == "regex":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	248 gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	249 #else if str($diffgtest.set_a.meth.type) == "manual":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	250 gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	251 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	252
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	253 #if str($diffgtest.set_b.meth.type) == "cln":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	254 gfdat.B.use\$cln = string2numericvector( '$diffgtest.set_b.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	255 #else if str($diffgtest.set_b.meth.type) == "regex":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	256 gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	257 #else if str($diffgtest.set_b.meth.type) == "manual":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	258 gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	259 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	260
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	261 #if str($diffgtest.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	262 plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	263 plotdiffg\$padj = as.logical( '$diffgtest.use.plotdiffg_padj' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	264 plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	265 plotdiffg\$show_names = as.logical( '$diffgtest.use.plotdiffg_show_names' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	266 #if $diffgtest.use.plotdiffg_mthr
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	267 plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	268 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	269 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	270 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	271
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	272 out.pdf='${outpdf}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	273 ]]></token>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	274 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	275
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	276 in.rdat = readRDS('${inputrds}')
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	277
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	278 pstc.projc = formals(projcells)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	279 pstc.projc\$knn = as.integer( '$projcell.knn' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	280 pstc.projc\$cthr = as.integer( '$projcell.cthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	281 #if str($projcell.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	282 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	283 pstc.projc\$fr = as.logical( '$projcell.use.fr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	284 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	285
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	286 pstc.projb = formals(projback)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	287 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	288 #if str($projback.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	289 pstc.projb\$fast = as.logical( '$projback.use.fast' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	290 pstc.projb\$rseed = as.integer( '$projback.use.rseed' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	291 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	292
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	293 pstc.comppval = formals(comppvalue)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	294 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	295 pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	296
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	297 pstc.plotgraph = formals(plotgraph)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	298 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	299 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	300 #if str($plotgraph.use.def) == "no":
6 c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af" iuc parents: 4 diff changeset	301 ##pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	302 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	303 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	304
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	305 pstc.compscore = formals(compscore)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	306 pstc.compscore\$nn = as.integer( '$compscore.nn' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	307 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	308
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	309 out.pdf='${outpdf}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	310 out.rdat='${outrdat}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	311 ]]></token>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	312 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	313 in.rdat = readRDS('${inputrds}')
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	314
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	315 perform.stemid = FALSE
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	316 perform.fateid = FALSE
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	317 perform.fateid.sominspect = FALSE
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	318
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	319 #if str($trjsid.basic.doit) == "yes"
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	320 perform.stemid = TRUE
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	321 trjsid.getproj = formals(getproj)
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	322
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	323 trjsid.numdiffgenes = 10
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	324 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	325 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	326
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	327 #if str($trjsid.basic.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	328
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	329 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	330 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	331
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	332 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	333 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	334
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	335 #if str($trjfid.basic.doit) == "yes":
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	336 perform.fateid = TRUE
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	337 trjfid_cellsfrom = formals(cellsfromtree)
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	338 trjfid_filterset = formals(filterset)
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	339 trjfid_getsom = formals(getsom)
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	340 trjfid_procsom = formals(procsom)
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	341 trjfid_plotheat = list()
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	342
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	343 trjfid_cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	344 #if str($trjfid.basic.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	345
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	346 trjfid_filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	347 trjfid_filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	348 trjfid_getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	349 trjfid_getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	350 trjfid_procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	351 trjfid_procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	352 trjfid_plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	353 trjfid_plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	354 trjfid_plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	355 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	356
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	357 #if str($trjfid.basic.som.doit) == "yes":
9 a6821f856a1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf iuc parents: 6 diff changeset	358 perform.fateid.sominspect = TRUE
4 86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	359
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	360 trjfidsomi = list()
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	361 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	362 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	363 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	364 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	365 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	366
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	367 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	368 trjfidsomi\$name = '$trjfid.basic.som.title'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	369
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	370 #if str($trjfid.basic.som.use.def) == "no":
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	371 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	372 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	373 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	374 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	375 #end if
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	376
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	377 out.pdf = '${outpdf}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	378 out.diffgenes = '${outdiffgenes}'
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	379
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	380 ]]></token>
86e2358cf273 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059" iuc parents: diff changeset	381 </macros>

Mercurial > repos > iuc > raceid_inspecttrajectory

annotate macros_cheetah.xml @ 9:a6821f856a1e draft