Mercurial > repos > iuc > raceid_inspectclusters

annotate macros_cheetah.xml @ 10:c7ddb719554d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:10 +0000
parents f3eb2291da05
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
1 <macros>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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2 <token name="@FILTNORM_CHEETAH@"><![CDATA[
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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3 ## Perform do.filter
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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4 use.filtnormconf = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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5
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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6 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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7 use.cluster = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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8
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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9 in.table = read.table(
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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10 '${intable}',
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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11 stringsAsFactors = F,
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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12 na.strings=c("NA", "-", "?", "."),
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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13 sep='\t',
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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14 header=TRUE,
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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15 row.names=1
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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16 )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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17
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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18 ## Hidden flag to use test data instead
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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19 ## see: test-data/use.intestinal
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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20
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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21 use.test.data = (names(in.table)[1] == "test")
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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22
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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23 sc = NULL
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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24 if (use.test.data) {
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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25 sc = SCseq(intestinalData)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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26 message("Loading test data from library")
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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27 } else {
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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28 sc = SCseq(in.table)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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29 }
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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30
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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31
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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32 filt = formals(filterdata)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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33 filt.ccc = formals(CCcorrect)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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34 filt.use.ccorrect = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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35 filt.lbatch.regexes = NULL
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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36
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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37 filt.geqone = as.logical( '$filt.hist_geq_one' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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38 filt\$mintotal = as.integer( '$filt.mintotal' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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39 filt\$minexpr = as.integer( '$filt.minexpr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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40 filt\$minnumber = as.integer( '$filt.minnumber' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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41 #if str($filt.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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42 filt\$knn = as.integer( '$filt.use.knn' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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43 filt\$ccor = as.numeric( '$filt.use.ccor' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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44 filt\$bmode = as.character( '$filt.use.bmode' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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45 #if $filt.use.LBatch_regexes:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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46 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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47 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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48 #if $filt.use.CGenes:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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49 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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50 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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51 #if $filt.use.FGenes:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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52 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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53 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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54 #if str($filt.use.ccc.use) == "yes"
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55 filt.use.ccorrect = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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56 #if $filt.use.ccc.vset:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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57 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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58 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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59 #if $filt.use.ccc.ncomp:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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60 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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61 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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62 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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63 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
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64 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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65 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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66 filt.ccc\$logscale = as.logical( '$filt.use.ccc.logscale' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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67 #end if
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68 #end if
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69
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70 out.pdf = '${outpdf}'
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71 out.rdat = '${outrdat}'
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72 out.table = '${outtable}'
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73
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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74 ]]></token>
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75 <token name="@CLUSTER_CHEETAH@"><![CDATA[
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76
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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77 in.rdat = readRDS('${inputrds}')
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78
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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79 sc = in.rdat
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80
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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81 ## Perform do.filter
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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82 use.filtnormconf = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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83
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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84 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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85 use.cluster = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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86
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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87
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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88 clust.compdist = formals(compdist)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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diff changeset
89 clust.clustexp = formals(clustexp)
20f522154663 "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' )
20f522154663 "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( '$clust.funcluster' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
92
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
93 #if str($clust.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
94
20f522154663 "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' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
96 #if $clust.use.knn:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
97 clust.compdist\$knn = as.integer( '$clust.use.knn' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
98 #end if
20f522154663 "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' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
100 #if $clust.use.samp:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
101 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
102 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
103 #if $clust.use.cln:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
104 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
20f522154663 "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( '$clust.use.clustnr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
107 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
108 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
109
20f522154663 "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
20f522154663 "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)
20f522154663 "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)
20f522154663 "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)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
114
20f522154663 "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( '$outlier.outminc' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
116 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
20f522154663 "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( '$outlier.final' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
118
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
119 #if str($outlier.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
120 #if $outlier.use.nbtree:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
121 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
122 #end if
20f522154663 "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( '$outlier.use.probthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
124 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
20f522154663 "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( '$outlier.use.rfseed' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
126 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
127 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
128
6
41f34e925bd5 "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
20f522154663 "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)
20f522154663 "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)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
132
20f522154663 "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( '$tsne.perplexity' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
134 cluster.compfr\$knn = as.integer( '$tsne.knn' )
6
41f34e925bd5 "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( '$tsne.umap_nn' )
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
136 #if str($tsne.use.def) == "no":
20f522154663 "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( '$tsne.use.initial_cmd' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
138 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
20f522154663 "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( '$tsne.use.rseed_fr' )
6
41f34e925bd5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents: 4
diff changeset
140 cluster.compumap\$n_epochs = as.integer( '$tsne.use.umap_epochs' )
41f34e925bd5 "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( '$tsne.use.umap_min_dist' )
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
142 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
143
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
144 genelist.tablelim = as.integer( '$extra.tablelim' )
20f522154663 "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( '$extra.plotlim' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
146 genelist.foldchange = as.integer( '$extra.foldchange' )
20f522154663 "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( '$extra.pvalue' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
148
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
149 out.pdf = '${outpdf}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
150 out.rdat = '${outrdat}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
151 out.genelist = '${outgenelist}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
152 out.assignments = '${outassignments}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
153 out.log = '${outlog}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
154
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
155 ]]>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
156 </token>
20f522154663 "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[
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
158 in.rdat = readRDS('${inputrds}')
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
159
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
160 perform.plotting = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
161 perform.symbolmap = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
162 perform.genesofinterest = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
163 perform.diffgene = FALSE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
164
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
165 #if str($plotgen.do_opt) == "yes":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
166 perform.plotting = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
167 plotting.cln = string2numericvector( '$plotgen.clusts_plot' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
168 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
169
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
170 #if str($plotsym.do_opt) == "yes":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
171 perform.symbolmap = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
172 plotsym = formals(plotsymbolsmap)
20f522154663 "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
20f522154663 "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
20f522154663 "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( '$plotsym.types_regex' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
176 #if str($plotsym.use.def) == "no":
20f522154663 "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' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
178 #if $plotsym.use.subset_regex:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
179 plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
180 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
181 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
182 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
183
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
184 #if str($gois.do_opt) == "yes":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
185 perform.genesofinterest = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
186 plotexp = formals(plotexpmap)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
187 plotmarkg = formals(plotmarkergenes)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
188
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
189 inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
20f522154663 "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
20f522154663 "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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
192
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
193 #if $gois.inspect_goi_cells:
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
194 inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
20f522154663 "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
20f522154663 "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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
197 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
198 #if str($gois.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
199 inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
20f522154663 "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
20f522154663 "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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
202 #if $gois.use.plotmarkg_cl
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
203 plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
204 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
205 #if $gois.use.plotmarkg_cap
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
206 plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
207 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
208 #if $gois.use.plotmarkg_flo
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
209 plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
210 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
211 #if $gois.use.plotmarkg_samples
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
212 plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
213 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
214 #if $gois.use.plotexp_n
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
215 plotexp\$n = as.character( '$gois.use.plotexp_n' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
216 #end if
20f522154663 "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( '$gois.use.plotmarkg_cthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
218 plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
20f522154663 "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( '$gois.use.plotmarkg_aggr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
220 plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
20f522154663 "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( '$gois.use.plotmarkg_cluster_cols' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
222 plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
20f522154663 "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( '$gois.use.plotmarkg_cluster_set' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
224 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
225 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
226
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
227 #if str($diffgtest.do_opt) == "yes":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
228 plotdiffg = formals(plotdiffgenesnb)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
229
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
230 perform.diffgene = TRUE
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
231 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
232 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
6
41f34e925bd5 "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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
234
20f522154663 "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()
20f522154663 "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()
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
237
20f522154663 "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
20f522154663 "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
20f522154663 "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
20f522154663 "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
20f522154663 "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
20f522154663 "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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
244
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
245 #if str($diffgtest.set_a.meth.type) == "cln":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
246 gfdat.A.use\$cln = string2numericvector( '$diffgtest.set_a.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
247 #else if str($diffgtest.set_a.meth.type) == "regex":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
248 gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
249 #else if str($diffgtest.set_a.meth.type) == "manual":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
250 gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
251 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
252
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
253 #if str($diffgtest.set_b.meth.type) == "cln":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
254 gfdat.B.use\$cln = string2numericvector( '$diffgtest.set_b.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
255 #else if str($diffgtest.set_b.meth.type) == "regex":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
256 gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
257 #else if str($diffgtest.set_b.meth.type) == "manual":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
258 gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
259 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
260
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
261 #if str($diffgtest.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
262 plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
20f522154663 "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( '$diffgtest.use.plotdiffg_padj' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
264 plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
20f522154663 "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' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
266 #if $diffgtest.use.plotdiffg_mthr
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
267 plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
268 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
269 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
270 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
271
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
272 out.pdf='${outpdf}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
273 ]]></token>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
274 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
275
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
276 in.rdat = readRDS('${inputrds}')
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
277
20f522154663 "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)
20f522154663 "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( '$projcell.knn' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
280 pstc.projc\$cthr = as.integer( '$projcell.cthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
281 #if str($projcell.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
282 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
20f522154663 "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( '$projcell.use.fr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
284 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
285
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
286 pstc.projb = formals(projback)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
287 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
288 #if str($projback.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
289 pstc.projb\$fast = as.logical( '$projback.use.fast' )
20f522154663 "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( '$projback.use.rseed' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
291 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
292
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
293 pstc.comppval = formals(comppvalue)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
294 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
20f522154663 "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( '$comppval.sensitive' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
296
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
297 pstc.plotgraph = formals(plotgraph)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
298 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
20f522154663 "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( '$plotgraph.scthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
300 #if str($plotgraph.use.def) == "no":
6
41f34e925bd5 "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( '$plotgraph.use.showtsne' )
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
302 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
303 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
304
20f522154663 "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)
20f522154663 "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( '$compscore.nn' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
307 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
308
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
309 out.pdf='${outpdf}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
310 out.rdat='${outrdat}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
311 ]]></token>
20f522154663 "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[
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
313 in.rdat = readRDS('${inputrds}')
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
314
9
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
parents: 6
diff changeset
315 perform.stemid = FALSE
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
parents: 6
diff changeset
316 perform.fateid = FALSE
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
parents: 6
diff changeset
317 perform.fateid.sominspect = FALSE
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
318
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
319 #if str($trjsid.basic.doit) == "yes"
9
f3eb2291da05 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
20f522154663 "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)
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
322
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
323 trjsid.numdiffgenes = 10
20f522154663 "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( '$trjsid.basic.i' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
325 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
326
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
327 #if str($trjsid.basic.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
328
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
329 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
20f522154663 "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( '$trjsid.basic.use.ndiffgenes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
331
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
332 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
333 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
334
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
335 #if str($trjfid.basic.doit) == "yes":
9
f3eb2291da05 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
f3eb2291da05 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)
f3eb2291da05 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)
f3eb2291da05 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)
f3eb2291da05 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)
f3eb2291da05 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
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
342
9
f3eb2291da05 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( '$trjfid.basic.cellsfromz' )
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
344 #if str($trjfid.basic.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
345
9
f3eb2291da05 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( '$trjfid.basic.use.filterset_minexpr' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
parents: 6
diff changeset
347 trjfid_filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
f3eb2291da05 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( '$trjfid.basic.use.getsom_nb' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
parents: 6
diff changeset
349 trjfid_getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
f3eb2291da05 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( '$trjfid.basic.use.procsom_corthr' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
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351 trjfid_procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
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352 trjfid_plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
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parents: 6
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353 trjfid_plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
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parents: 6
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354 trjfid_plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
4
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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355 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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356
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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357 #if str($trjfid.basic.som.doit) == "yes":
9
f3eb2291da05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
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358 perform.fateid.sominspect = TRUE
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20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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359
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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360 trjfidsomi = list()
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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361 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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362 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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363 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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364 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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365 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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366
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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367 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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368 trjfidsomi\$name = '$trjfid.basic.som.title'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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369
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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370 #if str($trjfid.basic.som.use.def) == "no":
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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371 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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372 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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373 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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374 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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375 #end if
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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376
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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377 out.pdf = '${outpdf}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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378 out.diffgenes = '${outdiffgenes}'
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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379
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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parents:
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380 ]]></token>
20f522154663 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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381 </macros>