Mercurial > repos > iuc > ggplot2_heatmap2

annotate heatmap2.xml @ 4:b718455b9541 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
author iuc
date Mon, 11 Feb 2019 17:27:39 -0500
parents f86777d8ba62
children f4899d509faa
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
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1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@">
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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3 <token name="@VERSION@">3.0.1</token>
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 </macros>
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5 <requirements>
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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6 <requirement type="package" version="@VERSION@">r-gplots</requirement>
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7 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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8 </requirements>
0
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9 <command detect_errors="exit_code"><![CDATA[
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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10 cat '$script' &&
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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11 Rscript '$script'
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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12 ]]></command>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 <configfiles>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14 <configfile name="script"><![CDATA[
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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15 ## Setup R error handling to go to stderr
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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16 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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17
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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18 ## Unify locale settings
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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21 ## Import library
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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22 library("RColorBrewer")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 library("gplots")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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25 input <- read.delim('$input1', sep='\t', header=TRUE)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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27 mat_input <- data.matrix(input[,2:ncol(input)])
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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28 rownames(mat_input) <- input[,1]
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30 #if $transform == "none"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31 linput <- mat_input
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32 #elif $transform == "log2"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 linput <- log2(mat_input)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 #elif $transform == "log2plus1"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 linput <- log2(mat_input+1)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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36 #elif $transform == "log10"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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37 linput <- log10(mat_input)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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38 #elif $transform == "log10plus1"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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39 linput <- log10(mat_input+1)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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40 #end if
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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42 #if $colorscheme == "whrd"
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43 colorscale = colfunc <- colorRampPalette(c("white", "red"))
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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44 #elif $colorscheme == "whblu"
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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45 colorscale = colfunc <- colorRampPalette(c("white", "blue"))
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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46 #elif $colorscheme == "blwhre"
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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47 colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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48 #end if
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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49
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50 #if $labels== "both"
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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51 rlabs = NULL
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52 clabs = NULL
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53 #elif $labels== "rows"
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54 rlabs = NULL
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55 clabs = FALSE
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56 #elif $labels== "columns"
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b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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57 rlabs = FALSE
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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58 clabs = NULL
0
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59 #elif $labels== "none"
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60 rlabs = FALSE
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61 clabs = FALSE
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62 #end if
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63
4
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64 pdf(file='$output1')
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65 colorscale
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66
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67 #if $cluster_cond.cluster:
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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68 hclust_fun = function(x) hclust(x, method='$cluster_cond.clustering')
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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69 dist_fun = function(x) dist(x, method='$cluster_cond.distance')
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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70 #if $cluster_cond.cluster_cols_rows=="rows":
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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71 heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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72 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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73 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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74 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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75 #elif $cluster_cond.cluster_cols_rows=="columns":
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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76 heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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77 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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78 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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79 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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80 #else
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81 heatmap.2(linput,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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82 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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83 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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84 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
b718455b9541 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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85 #end if
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86 #else
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87 heatmap.2(linput,
3
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88 dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs,
4
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89 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
1
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90 main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
0
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91 #end if
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92
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93 dev.off()
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94 ]]></configfile>
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95 </configfiles>
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96
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97 <inputs>
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98 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
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99 <param name="title" type="text" format="txt" label="Plot title"/>
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100 <param name="key" type="text" format="txt" label="key title"/>
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101 <param name="transform" type="select" label="Data transformation">
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102 <option value="none">Plot the data as it is</option>
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103 <option value="log2">Log2(value) transform my data</option>
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104 <option value="log2plus1">Log2(value+1) transform my data</option>
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105 <option value="log10">Log10(value) transform my data</option>
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106 <option value="log10plus1">Log10(value+1) transform my data</option>
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107 </param>
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108 <conditional name="cluster_cond">
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109 <param name="cluster" type="select" label="Enable data clustering">
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110 <option value="true">Yes</option>
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111 <option value="">No</option>
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112 </param>
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113 <when value="true">
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114 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
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115 <option value="both" selected="true">Cluster rows and columns</option>
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116 <option value="rows">Cluster rows and not columns</option>
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117 <option value="columns">Cluster columns and not rows</option>
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118 </param>
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119 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
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120 <option value="euclidean" selected="true">Euclidean</option>
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121 <option value="maximum">Maximum</option>
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122 </param>
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123 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
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124 <option value="complete" selected="true">Complete</option>
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125 <option value="average">Average</option>
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126 </param>
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127 </when>
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128 <when value=""/>
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129 </conditional>
0
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130 <param name="labels" type="select" label="Labeling columns and rows" >
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131 <option value="both" selected="true">Label my columns and rows</option>
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132 <option value="rows">Label rows and not columns</option>
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133 <option value="columns">Label columns and not rows</option>
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134 <option value="none">Do not label rows or columns</option>
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135 </param>
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136 <param name="colorscheme" type="select" label="Coloring groups" >
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137 <option value="whrd" selected="true">White to red</option>
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138 <option value="whblu">White to blue</option>
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139 <option value="blwhre">Blue to white to red</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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140 </param>
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141 <param name="scale" type="select" label="Data scaling" >
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142 <option value="none" selected="true">Do not scale my data</option>
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143 <option value="row">Scale my data by row</option>
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144 <option value="column">Scale my data by column</option>
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145 </param>
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146 </inputs>
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147 <outputs>
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148 <data name="output1" format="pdf"/>
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149 </outputs>
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150 <tests>
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151 <test>
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152 <param name="input1" value="mtcars.txt"/>
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153 <param name="cluster" value="true"/>
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154 <output name="output1" file="result1.pdf" compare="sim_size"/>
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155 </test>
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156 <test>
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157 <param name="input1" value="mtcars.txt"/>
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158 <param name="cluster" value=""/>
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159 <output name="output1" file="result2.pdf" compare="sim_size"/>
0
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160 </test>
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161 </tests>
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162 <help><![CDATA[
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163 This tool employs the heatmap.2 function from the R gplots package and will generate a heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance method and the Complete hierarchical clustering method by default.
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164
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165 Input data should have row labels in the first column and column labels. For example, the row labels (the first column) should represent gene IDs and the column labels should represent sample IDs.
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166 ]]></help>
2
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167 <citations>
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168 </citations>
0
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169 </tool>