Mercurial > repos > iuc > ggplot2_heatmap2

annotate heatmap2.xml @ 3:f86777d8ba62 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 381fece97cb737e110e75e85fd0b6ebfc90f9c36
author iuc
date Sat, 28 Jul 2018 03:42:35 -0400
parents 672eb1c4314c
children b718455b9541
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f86777d8ba62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 381fece97cb737e110e75e85fd0b6ebfc90f9c36
iuc
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1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@+galaxy1">
0
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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2 <macros>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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3 <import>macros.xml</import>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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4 </macros>
2
672eb1c4314c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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5 <requirements>
0
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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6 <requirement type="package" version="3.0.1">r-gplots</requirement>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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 '$script' &&
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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11 Rscript '$script' &&
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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12 mv output_plot.pdf $output1
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 ]]></command>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14 <configfiles>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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15 <configfile name="script"><![CDATA[
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17 @R_INIT@
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18
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19 ## Import library
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20 library("RColorBrewer")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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21 library("gplots")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 input <- read.delim('$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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24
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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25 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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26 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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27
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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28 hclust_fun = function(x) hclust(x, method="complete")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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29 dist_fun = function(x) dist(x, method="maximum")
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30 distfun=dist_fun
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31 hclustfun=hclust_fun
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 #if $transform == "none"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 linput <- mat_input
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 #elif $transform == "log2"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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36 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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37 #elif $transform == "log2plus1"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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38 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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39 #elif $transform == "log10"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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40 linput <- log10(mat_input)
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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41 #elif $transform == "log10plus1"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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42 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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43 #end if
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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44
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45 #if $colorscheme == "whrd"
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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46 colorscale = colfunc <- colorRampPalette(c("white", "red"))
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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47 #elif $colorscheme == "whblu"
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48 colorscale = colfunc <- colorRampPalette(c("white", "blue"))
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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49 #elif $colorscheme == "blwhre"
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50 colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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51 #end if
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52
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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53 #if $labels== "both"
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54 rlabs = NULL
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55 clabs = NULL
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56 #elif $labels== "rows"
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57 rlabs = NULL
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58 clabs = FALSE
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59 #elif $labels== "columns"
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60 rlabs = FALSE
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61 clabs = NULL
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62 #elif $labels== "none"
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63 rlabs = FALSE
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64 clabs = FALSE
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65 #end if
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66
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67 pdf(file='output_plot.pdf')
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68 colorscale
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69
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70 #if $cluster:
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71 heatmap.2(linput,
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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72 distfun=dist_fun, hclustfun=hclust_fun, scale = '$scale', labRow = rlabs, labCol = clabs,
1
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73 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
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74 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
0
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75 #else
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76 heatmap.2(linput,
3
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77 dendrogram="none", Colv=FALSE, Rowv=FALSE, scale = '$scale', labRow = rlabs, labCol = clabs,
1
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78 col=colfunc(50), trace="none", density.info = "none", margins=c(8,8),
d76c7d77e629 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 97544038b04c02170ab82877db666fa3022e4469
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79 main='$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=45)
0
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80 #end if
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81
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82 dev.off()
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83
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84 ]]></configfile>
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85 </configfiles>
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86
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87 <inputs>
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88 <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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89 <param name="title" type="text" format="txt" label="Plot title"/>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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90 <param name="key" type="text" format="txt" label="key title"/>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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91 <expand macro="transform" />
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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92 <param name="cluster" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable data clustering" />
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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93 <param name="labels" type="select" label="Labeling columns and rows" >
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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94 <option value="both" selected="True">Label my columns and rows</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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95 <option value="rows">Label rows and not columns</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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96 <option value="columns">Label columns and not rows</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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97 <option value="none">Do not label rows or columns</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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98 </param>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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99 <param name="colorscheme" type="select" label="Coloring groups" >
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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100 <option value="whrd" selected="True">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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101 <option value="whblu">White to blue</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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102 <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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103 </param>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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104 <param name="scale" type="select" label="Data scaling" >
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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105 <option value="none" selected="True">Do not scale my data</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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106 <option value="row">Scale my data by row</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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107 <option value="column">Scale my data by column</option>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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108 </param>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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109 </inputs>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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110 <outputs>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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111 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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112 </outputs>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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113 <tests>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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114 <test>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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115 <param name="input1" value="mtcars.txt"/>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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116 <output name="output1" file="ggplot_heatmap2_result1.pdf" compare="sim_size"/>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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117 </test>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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118 </tests>
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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119 <help><![CDATA[
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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120 This tool will generate a clustered heatmap of your data. More customization options will be added, for now the heatmap uses a red coloring scheme and clustering is performed using the "maximum" similarity measure and the "complete" hierarchical clustering measure.
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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121
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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122 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.
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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123
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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124 This wrapper employs the heatmap.2 function of R.
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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125 ]]></help>
2
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126 <citations>
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127 </citations>
0
176183828671 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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128 </tool>