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annotate heatmap.xml @ 0:22d5d811dc37 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
author artbio
date Sat, 20 Jul 2019 17:55:20 -0400
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22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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1 <tool id="high_dim_heatmap" name="Plot heatmap" version="1.0.0">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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2 <description>with high number of rows</description>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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3 <requirements>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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4 <requirement type="package" version="3.0.1">r-gplots</requirement>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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5 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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6 </requirements>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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7 <command detect_errors="exit_code"><![CDATA[
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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8 cat '$script' &&
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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9 Rscript '$script'
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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10 ]]></command>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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11 <configfiles>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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12 <configfile name="script"><![CDATA[
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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13 ## Setup R error handling to go to stderr
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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14 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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15
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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16 ## Unify locale settings
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17 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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18
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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19 ## Import library
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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20 library("RColorBrewer")
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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21 library("gplots")
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22
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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23 input <- read.delim('$input1', sep='\t', header=TRUE)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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24
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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25 mat_input <- data.matrix(input[,2:ncol(input)])
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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26 rownames(mat_input) <- input[,1]
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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27
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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28 #if $transform == "none"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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29 linput <- mat_input
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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30 #elif $transform == "log2"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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31 linput <- log2(mat_input)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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32 #elif $transform == "log2plus1"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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33 linput <- log2(mat_input+1)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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34 #elif $transform == "log10"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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35 linput <- log10(mat_input)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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36 #elif $transform == "log10plus1"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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37 linput <- log10(mat_input+1)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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38 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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39
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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40 #if $colorscheme == "whrd"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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41 colorscale = colfunc <- colorRampPalette(c("white", "red"))
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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42 #elif $colorscheme == "whblu"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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43 colorscale = colfunc <- colorRampPalette(c("white", "blue"))
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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44 #elif $colorscheme == "blwhre"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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45 colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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46 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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47
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48 #if $labels== "both"
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49 rlabs = NULL
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50 clabs = NULL
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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51 #elif $labels== "rows"
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52 rlabs = NULL
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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53 clabs = FALSE
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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54 #elif $labels== "columns"
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55 rlabs = FALSE
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56 clabs = NULL
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57 #elif $labels== "none"
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58 rlabs = FALSE
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59 clabs = FALSE
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60 #end if
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61
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62 pdf(file='$output1', paper='special', height=$height)
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63 colorscale
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64
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65 #if $cluster_cond.cluster:
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66 hclust_fun = function(x) hclust(x, method='$cluster_cond.clustering')
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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67 dist_fun = function(x) dist(x, method='$cluster_cond.distance')
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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68 #if $cluster_cond.cluster_cols_rows=="rows":
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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69 heatmap.2(linput, dendrogram="row", Colv=FALSE, Rowv=TRUE,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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70 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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71 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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72 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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73 lhei=c(1, $lineheight))
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74 #elif $cluster_cond.cluster_cols_rows=="columns":
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75 heatmap.2(linput, dendrogram="column", Colv=TRUE, Rowv=FALSE,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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76 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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77 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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78 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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79 lhei=c(1, $lineheight))
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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80 #else
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81 heatmap.2(linput,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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82 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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83 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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84 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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85 lhei=c(1, $lineheight))
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86 #end if
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87 #else
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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88 heatmap.2(linput,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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89 dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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90 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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91 main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = $rowfontsize, srtCol=45,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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92 lhei=c(1, $lineheight))
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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93 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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94
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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95 dev.off()
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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96 ]]></configfile>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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97 </configfiles>
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98
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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99 <inputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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100 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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101 <param name="title" type="text" format="txt" label="Plot title"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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102 <param name="key" type="text" format="txt" label="key title"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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103 <param name="transform" type="select" label="Data transformation">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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104 <option value="none">Plot the data as it is</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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105 <option value="log2">Log2(value) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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106 <option value="log2plus1">Log2(value+1) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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107 <option value="log10">Log10(value) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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108 <option value="log10plus1">Log10(value+1) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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109 </param>
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110 <conditional name="cluster_cond">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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111 <param name="cluster" type="select" label="Enable data clustering">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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112 <option value="true">Yes</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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113 <option value="">No</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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114 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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115 <when value="true">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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116 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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117 <option value="both" selected="true">Cluster rows and columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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118 <option value="rows">Cluster rows and not columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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119 <option value="columns">Cluster columns and not rows</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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120 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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121 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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122 <option value="euclidean" selected="true">Euclidean</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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123 <option value="maximum">Maximum</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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124 </param>
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artbio
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125 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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126 <option value="complete" selected="true">Complete</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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127 <option value="average">Average</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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128 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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129 </when>
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130 <when value=""/>
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artbio
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131 </conditional>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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132 <param name="labels" type="select" label="Labeling columns and rows" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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133 <option value="both" selected="true">Label my columns and rows</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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134 <option value="rows">Label rows and not columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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135 <option value="columns">Label columns and not rows</option>
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artbio
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136 <option value="none">Do not label rows or columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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137 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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138 <param name="colorscheme" type="select" label="Coloring groups" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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139 <option value="whrd" selected="true">White to red</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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140 <option value="whblu">White to blue</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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141 <option value="blwhre">Blue to white to red</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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142 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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143 <param name="scale" type="select" label="Data scaling" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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144 <option value="none" selected="true">Do not scale my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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145 <option value="row">Scale my data by row</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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146 <option value="column">Scale my data by column</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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147 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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148
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149 <param name="height" type="float" label="tweak plot height" value="7" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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150 <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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151 <param name="lineheight" type="integer" label="tweak line height" value="4" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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152 </inputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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153 <outputs>
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154 <data name="output1" format="pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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155 </outputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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156 <tests>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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157 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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158 <param name="input1" value="mtcars.txt"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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159 <param name="cluster" value="true"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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160 <output name="output1" file="result1.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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161 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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162 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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163 <param name="input1" value="mtcars.txt"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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164 <param name="cluster" value=""/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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165 <output name="output1" file="result2.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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166 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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167 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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168 <param name="input1" value="complex_table.tsv"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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169 <param name="transform" value="log2plus1"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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170 <param name="cluster" value=""/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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171 <param name="colorscheme" value="blwhre"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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172 <param name="height" value="21"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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173 <param name="rowfontsize" value="0.4"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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174 <param name="lineheight" value="15"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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175 <output name="output1" file="complex_result1.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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176 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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177 </tests>
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178 <help><![CDATA[
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179 This tool employs the heatmap.2 function from the R gplots package and will generate a
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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180 heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance
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181 method and the Complete hierarchical clustering method by default.
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182
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183 Input data should have row labels in the first column and column labels. For example,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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184 the row labels (the first column) should represent gene IDs and the column labels should
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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185 represent sample IDs.
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186
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187 To adapt heatmap.2 to high number of lines, tweak the parameters:
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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188
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189 - `tweak plot height`. By default 7 (inches), this can be increased to 14, 21, 28, etc..
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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190 - `tweak row label size`. By default 0.8. This is usually diminished to 0.3, 0.1, etc to
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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191 adapt the label font to high number of rows
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192 - `tweak line height`. By default 4. This is a metric to define the relative size of the
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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193 heatmap panel in the plot layout. This is a bit tricky to adjust, but should be adapted
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194 when plot height is increased (typically to 8, 10, 15, etc...)
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195
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196 For instance, upload the dataset
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197 https://raw.githubusercontent.com/ARTbio/tools-artbio/master/tools/high_dim_heatmap/test-data/complex_table.tsv
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198 to your account and test this tools with:
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199
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200 - `tweak plot height` : 21.0
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201 - `tweak row label size`: 0.4
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202 - `tweak line height`: 14
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203
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204
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205 ]]></help>
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206 <citations>
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207 </citations>
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208 </tool>