Mercurial > repos > iuc > raceid_clustering

annotate macros_cheetah.xml @ 5:7e014059a88d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 1ad3837c2251aba8bd997386c3c27f6cd5b1c9e7"
author iuc
date Wed, 29 Jan 2020 17:16:36 -0500
parents ee0bbc160cb1
children a4b734cd253b
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ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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1 <macros>
ee0bbc160cb1 "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[
ee0bbc160cb1 "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
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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4 use.filtnormconf = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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5
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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6 ## Perform do.cluster, do.outlier, do.clustmap, mkgenelist
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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7 use.cluster = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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8
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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9 in.table = read.table(
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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10 '${intable}',
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11 stringsAsFactors = F,
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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12 na.strings=c("NA", "-", "?", "."),
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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13 sep='\t',
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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14 header=TRUE,
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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15 row.names=1
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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16 )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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17
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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18 ## Hidden flag to use test data instead
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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19 ## see: test-data/use.intestinal
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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20
ee0bbc160cb1 "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")
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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22
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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23 sc = NULL
ee0bbc160cb1 "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) {
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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25 sc = SCseq(intestinalData)
ee0bbc160cb1 "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")
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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27 } else {
ee0bbc160cb1 "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)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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29 }
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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30
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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31
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32 filt = formals(filterdata)
ee0bbc160cb1 "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)
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34 filt.use.ccorrect = FALSE
ee0bbc160cb1 "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
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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36
ee0bbc160cb1 "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' )
ee0bbc160cb1 "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( '$filt.mintotal' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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39 filt\$minexpr = as.integer( '$filt.minexpr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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40 filt\$minnumber = as.integer( '$filt.minnumber' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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41 #if str($filt.use.def) == "no":
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42 filt\$knn = as.integer( '$filt.use.knn' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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43 filt\$ccor = as.numeric( '$filt.use.ccor' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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44 filt\$bmode = as.character( '$filt.use.bmode' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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45 #if $filt.use.LBatch_regexes:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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46 filt.lbatch.regexes = string2textvector( '$filt.use.LBatch_regexes' )
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47 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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48 #if $filt.use.CGenes:
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49 filt\$CGenes = string2textvector( '$filt.use.CGenes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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50 #end if
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51 #if $filt.use.FGenes:
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52 filt\$FGenes = string2textvector( '$filt.use.FGenes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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53 #end if
ee0bbc160cb1 "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
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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56 #if $filt.use.ccc.vset:
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57 filt.ccc\$vset = string2textvector( '$filt.use.ccc.vset' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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58 #end if
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59 #if $filt.use.ccc.ncomp:
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60 filt.ccc\$nComp = as.integer( '$filt.use.ccc.ncomp' )
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61 #end if
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62 filt.ccc\$pvalue = as.numeric( '$filt.use.ccc.pvalue' )
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63 filt.ccc\$quant = as.numeric( '$filt.use.ccc.quant' )
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64 filt.ccc\$dimR = as.logical( '$filt.use.ccc.dimr' )
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65 filt.ccc\$mode = as.character( '$filt.use.ccc.mode.value' )
ee0bbc160cb1 "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( '$filt.use.ccc.logscale' )
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67 #end if
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68 #end if
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69
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70 out.pdf = '${outpdf}'
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71 out.rdat = '${outrdat}'
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72 out.table = '${outtable}'
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73
ee0bbc160cb1 "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
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77 in.rdat = readRDS('${inputrds}')
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78
ee0bbc160cb1 "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
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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81 ## Perform do.filter
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82 use.filtnormconf = FALSE
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83
ee0bbc160cb1 "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
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85 use.cluster = TRUE
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86
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
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diff changeset
87
ee0bbc160cb1 "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)
ee0bbc160cb1 "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)
ee0bbc160cb1 "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' )
ee0bbc160cb1 "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( '$clust.funcluster' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
92
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
93 #if str($clust.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
94
ee0bbc160cb1 "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' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
96 #if $clust.use.knn:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
97 clust.compdist\$knn = as.integer( '$clust.use.knn' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
98 #end if
ee0bbc160cb1 "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' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
100 #if $clust.use.samp:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
101 clust.clustexp\$samp = as.integer( '$clust.use.samp' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
102 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
103 #if $clust.use.cln:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
104 clust.clustexp\$cln = as.integer( '$clust.use.cln' )
ee0bbc160cb1 "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( '$clust.use.clustnr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
106 clust.clustexp\$bootnr = as.integer( '$clust.use.bootnr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
107 ##clust.clustexp\$rseed = as.integer( '$clust.use.rseed' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
108 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
109 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
110
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
111 outlier.use.randomforest = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
112 outlier.findoutliers = formals(findoutliers)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
113 outlier.clustheatmap = formals(clustheatmap)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
114 outlier.rfcorrect = formals(rfcorrect)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
115
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
116 outlier.findoutliers\$outminc = as.integer( '$outlier.outminc' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
117 outlier.findoutliers\$outlg = as.integer( '$outlier.outlg' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
118 outlier.rfcorrect\$final = as.logical( '$outlier.final' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
119
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
120 #if str($outlier.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
121 #if $outlier.use.nbtree:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
122 outlier.rfcorrect\$nbtree = as.integer( '$outlier.use.nbtree' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
123 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
124 outlier.findoutliers\$probthr = as.numeric( '$outlier.use.probthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
125 outlier.findoutliers\$outdistquant = as.numeric( '$outlier.use.outdistquant' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
126 ##outlier.rfcorrect\$rfseed = as.integer( '$outlier.use.rfseed' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
127 outlier.rfcorrect\$nbfactor = as.integer( '$outlier.use.nbfactor' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
128 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
129
ee0bbc160cb1 "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)
ee0bbc160cb1 "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)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
132
ee0bbc160cb1 "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( '$tsne.perplexity' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
134 cluster.compfr\$knn = as.integer( '$tsne.knn' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
135 #if str($tsne.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
136 cluster.comptsne\$initial_cmd = as.logical( '$tsne.use.initial_cmd' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
137 cluster.comptsne\$rseed = as.integer( '$tsne.use.rseed_tsne' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
138 cluster.compfr\$rseed = as.integer( '$tsne.use.rseed_fr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
139 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
140
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
141 genelist.tablelim = as.integer( '$extra.tablelim' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
142 genelist.plotlim = as.integer( '$extra.plotlim' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
143 genelist.foldchange = as.integer( '$extra.foldchange' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
144 genelist.pvalue = as.numeric( '$extra.pvalue' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
145
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
146 out.pdf = '${outpdf}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
147 out.rdat = '${outrdat}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
148 out.genelist = '${outgenelist}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
149 out.assignments = '${outassignments}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
150 out.log = '${outlog}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
151
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
152 ]]>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
153 </token>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
154 <token name="@INSPECTCLUSTERS_CHEETAH@"><![CDATA[
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
155 in.rdat = readRDS('${inputrds}')
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
156
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
157 perform.plotting = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
158 perform.symbolmap = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
159 perform.genesofinterest = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
160 perform.diffgene = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
161
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
162 #if str($plotgen.do_opt) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
163 perform.plotting = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
164 plotting.cln = string2numericvector( '$plotgen.clusts_plot' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
165 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
166
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
167 #if str($plotsym.do_opt) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
168 perform.symbolmap = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
169 plotsym = formals(plotsymbolsmap)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
170 plotsym.use.typeremoveregex = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
171 plotsym.use.typeremoveregex.subselect = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
172 plotsym.use.typeremoveregex = as.character( '$plotsym.types_regex' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
173 #if str($plotsym.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
174 plotsym\$fr = as.logical( '$plotsym.use.fr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
175 #if $plotsym.use.subset_regex:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
176 plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
177 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
178 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
179 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
180
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
181 #if str($gois.do_opt) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
182 perform.genesofinterest = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
183 plotexp = formals(plotexpmap)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
184 plotmarkg = formals(plotmarkergenes)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
185
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
186 inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
187 plotexp\$g = inspect.goi.use.genes
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
188 plotmarkg\$genes = inspect.goi.use.genes
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
189
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
190 #if $gois.inspect_goi_cells:
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
191 inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
192 plotexp\$cells = inspect.goi.use.cells
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
193 plotmarkg\$cells = inspect.goi.use.cells
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
194 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
195 #if str($gois.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
196 inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
197 plotexp\$imputed = inspect.goi.use.imputed
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
198 plotmarkg\$imputed = inspect.goi.use.imputed
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
199 #if $gois.use.plotmarkg_cl
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
200 plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
201 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
202 #if $gois.use.plotmarkg_cap
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
203 plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
204 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
205 #if $gois.use.plotmarkg_flo
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
206 plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
207 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
208 #if $gois.use.plotmarkg_samples
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
209 plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
210 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
211 #if $gois.use.plotexp_n
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
212 plotexp\$n = as.character( '$gois.use.plotexp_n' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
213 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
214 plotmarkg\$cthr = as.integer( '$gois.use.plotmarkg_cthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
215 plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
216 plotmarkg\$aggr = as.logical( '$gois.use.plotmarkg_aggr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
217 plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
218 plotmarkg\$cluster_cols = as.logical( '$gois.use.plotmarkg_cluster_cols' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
219 plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
220 plotmarkg\$cluster_set = as.logical( '$gois.use.plotmarkg_cluster_set' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
221 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
222 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
223
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
224 #if str($diffgtest.do_opt) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
225 plotdiffg = formals(plotdiffgenesnb)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
226
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
227 perform.diffgene = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
228 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
229 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
230
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
231 gfdat.A.use = list()
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
232 gfdat.B.use = list()
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
233
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
234 gfdat.A.use\$manual = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
235 gfdat.A.use\$regex = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
236 gfdat.A.use\$cln = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
237 gfdat.B.use\$manual = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
238 gfdat.B.use\$regex = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
239 gfdat.B.use\$cln = NULL
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
240
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
241 #if str($diffgtest.set_a.meth.type) == "cln":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
242 gfdat.A.use\$cln = string2numericvector( '$diffgtest.set_a.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
243 #else if str($diffgtest.set_a.meth.type) == "regex":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
244 gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
245 #else if str($diffgtest.set_a.meth.type) == "manual":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
246 gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
247 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
248
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
249 #if str($diffgtest.set_b.meth.type) == "cln":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
250 gfdat.B.use\$cln = string2numericvector( '$diffgtest.set_b.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
251 #else if str($diffgtest.set_b.meth.type) == "regex":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
252 gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
253 #else if str($diffgtest.set_b.meth.type) == "manual":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
254 gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
255 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
256
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
257 #if str($diffgtest.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
258 plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
259 plotdiffg\$padj = as.logical( '$diffgtest.use.plotdiffg_padj' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
260 plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
261 plotdiffg\$show_names = as.logical( '$diffgtest.use.plotdiffg_show_names' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
262 #if $diffgtest.use.plotdiffg_mthr
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
263 plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
264 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
265 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
266 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
267
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
268 out.pdf='${outpdf}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
269 ]]></token>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
270 <token name="@TRAJECTORY_CHEETAH@"><![CDATA[
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
271
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
272 in.rdat = readRDS('${inputrds}')
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
273
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
274 pstc.projc = formals(projcells)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
275 pstc.projc\$knn = as.integer( '$projcell.knn' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
276 pstc.projc\$cthr = as.integer( '$projcell.cthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
277 #if str($projcell.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
278 pstc.projc\$nmode = as.logical( '$projcell.use.nmode' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
279 pstc.projc\$fr = as.logical( '$projcell.use.fr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
280 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
281
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
282 pstc.projb = formals(projback)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
283 pstc.projb\$pdishuf = as.integer( '$projback.pdishuf' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
284 #if str($projback.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
285 pstc.projb\$fast = as.logical( '$projback.use.fast' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
286 pstc.projb\$rseed = as.integer( '$projback.use.rseed' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
287 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
288
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
289 pstc.comppval = formals(comppvalue)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
290 pstc.comppval\$pthr = as.numeric( '$comppval.pthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
291 pstc.comppval\$sensitive = as.logical( '$comppval.sensitive' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
292
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
293 pstc.plotgraph = formals(plotgraph)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
294 pstc.plotgraph\$showCells = as.logical( '$plotgraph.showcells' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
295 pstc.plotgraph\$scthr = as.numeric( '$plotgraph.scthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
296 #if str($plotgraph.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
297 pstc.plotgraph\$showTsne = as.logical( '$plotgraph.use.showtsne' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
298 pstc.plotgraph\$tp = as.numeric( '$plotgraph.use.tp' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
299 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
300
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
301 pstc.compscore = formals(compscore)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
302 pstc.compscore\$nn = as.integer( '$compscore.nn' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
303 pstc.compscore\$scthr = as.numeric( '$compscore.scthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
304
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
305 out.pdf='${outpdf}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
306 out.rdat='${outrdat}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
307 ]]></token>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
308 <token name="@INSPECTTRAJECTORIES_CHEETAH@"><![CDATA[
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
309 in.rdat = readRDS('${inputrds}')
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
310
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
311 perform.stemID = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
312 perform.fateID = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
313 perform.fateID.sominspect = FALSE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
314
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
315 #if str($trjsid.basic.doit) == "yes"
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
316 perform.stemID = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
317 trjsid.getproj = formals(getproj)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
318
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
319 trjsid.numdiffgenes = 10
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
320 trjsid.getproj\$i = as.integer( '$trjsid.basic.i' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
321 trjsid.branchcells.ijk = string2numericvector( '$trjsid.basic.br' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
322
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
323 #if str($trjsid.basic.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
324
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
325 trjsid.getproj\$zscore = as.logical( '$trjsid.basic.use.zscore' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
326 trjsid.numdiffgenes = as.integer( '$trjsid.basic.use.ndiffgenes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
327
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
328 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
329 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
330
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
331 #if str($trjfid.basic.doit) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
332 perform.fateID = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
333 trjfid.cellsfrom = formals(cellsfromtree)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
334 trjfid.filterset = formals(filterset)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
335 trjfid.getsom = formals(getsom)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
336 trjfid.procsom = formals(procsom)
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
337 trjfid.plotheat = list()
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
338
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
339 trjfid.cellsfrom\$z = string2numericvector( '$trjfid.basic.cellsfromz' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
340 #if str($trjfid.basic.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
341
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
342 trjfid.filterset\$minexpr = as.integer( '$trjfid.basic.use.filterset_minexpr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
343 trjfid.filterset\$minnumber = as.integer( '$trjfid.basic.use.filterset_minnumber' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
344 trjfid.getsom\$nb = as.numeric( '$trjfid.basic.use.getsom_nb' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
345 trjfid.getsom\$alpha = as.numeric( '$trjfid.basic.use.getsom_alpha' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
346 trjfid.procsom\$corthr = as.numeric( '$trjfid.basic.use.procsom_corthr' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
347 trjfid.procsom\$minsom = as.integer( '$trjfid.basic.use.procsom_minsom' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
348 trjfid.plotheat\$xgrid = as.logical( '$trjfid.basic.use.plotheat_xgrid' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
349 trjfid.plotheat\$ygrid = as.logical( '$trjfid.basic.use.plotheat_ygrid' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
350 trjfid.plotheat\$xlab = as.logical( '$trjfid.basic.use.plotheat_xlab' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
351 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
352
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
353 #if str($trjfid.basic.som.doit) == "yes":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
354 perform.fateID.sominspect = TRUE
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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355
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
356 trjfidsomi = list()
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
357 #if str($trjfid.basic.som.use_genes.typer) == "genelist":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
358 trjfidsomi.use.genes = string2textvector( '$trjfid.basic.som.use_genes.use_genes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
359 #else if str($trjfid.basic.som.use_genes.typer) == "cln":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
360 trjfidsomi.use.genes = as.integer( '$trjfid.basic.som.use_genes.use_genes' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
361 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
362
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
363 trjfidsomi.use.types = '$trjfid.basic.som.use_types'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
364 trjfidsomi\$name = '$trjfid.basic.som.title'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
365
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
366 #if str($trjfid.basic.som.use.def) == "no":
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
367 trjfidsomi\$cluster = as.logical( '$trjfid.basic.som.use.cluster' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
368 trjfidsomi\$alpha = as.numeric( '$trjfid.basic.som.use.alpha' )
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
369 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
370 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
371 #end if
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
372
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
373 out.pdf = '${outpdf}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
374 out.diffgenes = '${outdiffgenes}'
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
375
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
376 ]]></token>
ee0bbc160cb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
diff changeset
377 </macros>