Mercurial > repos > iuc > ggplot2_heatmap2

annotate heatmap2.xml @ 9:51c6ccaace7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 2c9e4e82700be2c9d5c703b385c2528369fb3eeb
author iuc
date Fri, 11 Oct 2024 13:12:37 +0000
parents 374e9062d874
children 48b42ee61bc5
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53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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76380bf74511 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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51c6ccaace7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 2c9e4e82700be2c9d5c703b385c2528369fb3eeb
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3 <token name="@TOOL_VERSION@">3.2.0</token>
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53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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4 <token name="@VERSION_SUFFIX@">0</token>
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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5 </macros>
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c6bfec911a41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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6 <requirements>
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566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
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7 <requirement type="package" version="@TOOL_VERSION@">r-gplots</requirement>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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8 <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
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c6bfec911a41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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9 </requirements>
0
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10 <command detect_errors="exit_code"><![CDATA[
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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11 cat '$script' &&
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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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12 Rscript '$script'
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 ]]></command>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14 <configfiles>
76380bf74511 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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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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16 ## Setup R error handling to go to stderr
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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17 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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18
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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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19 ## Unify locale settings
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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20 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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22 ## Import library
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 library("RColorBrewer")
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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24 library("gplots")
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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26 input <- read.delim('$input1', sep='\t', header=TRUE)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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28 mat_input <- data.matrix(input[,2:ncol(input)])
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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29 rownames(mat_input) <- input[,1]
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31 #if $transform == "none"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32 linput <- mat_input
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 #elif $transform == "log2"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 linput <- log2(mat_input)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 #elif $transform == "log2plus1"
76380bf74511 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+1)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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37 #elif $transform == "log10"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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38 linput <- log10(mat_input)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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39 #elif $transform == "log10plus1"
76380bf74511 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+1)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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41 #end if
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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42
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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43 #if $zscore_cond.zscore == "rows":
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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44 linput <- t(apply(linput, 1, scale))
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45 colnames(linput) <- colnames(input)[2:ncol(input)]
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46 rownames(linput) <- input[,1]
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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47 scale <- "none"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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48 #elif $zscore_cond.zscore == "cols":
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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49 linput <- apply(linput, 2, scale)
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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50 rownames(linput) <- input[,1]
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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51 scale <- "none"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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52 #elif $zscore_cond.zscore == "none":
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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53 scale <- "$zscore_cond.scale"
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54 #end if
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55
7
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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56 srtCol <- 30
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57 #if $labels == "both"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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58 rlabs <- NULL
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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59 clabs <- NULL
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60 label_margins <- c(8,8)
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61 #elif $labels == "rows"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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62 rlabs <- NULL
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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63 clabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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64 srtCol <- NULL
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65 label_margins <- c(1,8)
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66 #elif $labels == "columns"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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67 rlabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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68 clabs <- NULL
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69 label_margins <- c(8,1)
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3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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70 #elif $labels == "none"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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71 rlabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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72 clabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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73 srtCol <- NULL
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74 label_margins <- c(1,1)
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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75 #end if
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76
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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77 #if $cluster_cond.cluster == "yes":
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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78 dendrogramtoplot <- "$cluster_cond.cluster_cols_rows"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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79 #if $cluster_cond.cluster_cols_rows == "both"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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80 reorder_cols <- TRUE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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81 reorder_rows <- TRUE
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82 layout_matrix <- rbind(c(4,3), c(2,1))
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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83 key_margins <- list(mar=c(4,0.5,2,1))
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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84 lheight <- c(1, 5)
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
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85 lwidth <- c(1,3)
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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86 #elif $cluster_cond.cluster_cols_rows == "row"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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87 reorder_cols <- FALSE
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88 reorder_rows <- TRUE
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89 layout_matrix <- rbind(c(3,4), c(2,1))
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90 key_margins <- list(mar=c(3,5,1,10))
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91 lheight <- c(1,7)
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92 lwidth <- c(1,3)
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93 #elif $cluster_cond.cluster_cols_rows == "column"
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94 reorder_cols <- TRUE
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95 reorder_rows <- FALSE
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96 layout_matrix <- rbind(c(4), c(3), c(1), c(2))
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97 key_margins <- list(mar=c(4,0.5,2,1))
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98 lheight <- c(0.3, 2, 6, 1)
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99 lwidth <- c(1)
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100 #end if
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101 hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
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102 #if $cluster_cond.distance == 'pearson_correlation':
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103 dist_fun <- function(x) as.dist(1 - cor(t(x)))
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104 #elif $cluster_cond.distance == 'spearmann_correlation':
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105 dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman"))
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106 #else:
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107 dist_fun <- function(x) dist(x, method='$cluster_cond.distance')
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108 #end if
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109 #else:
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110 dendrogramtoplot <- "none"
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111 reorder_cols <- FALSE
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112 reorder_rows <- FALSE
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113 layout_matrix <- rbind(c(0,4,3), c(0,1,2))
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114 key_margins <- list(mar=c(3,5,1,10))
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115 lheight <- c(1,7)
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116 lwidth <- c(1,7,1)
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117 hclust_fun <- hclust
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118 dist_fun <- dist
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119 label_margins <- c(8,2)
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120 #end if
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121
5
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122 ncolors <- 50
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123 #if $colorchoice.type == "palettes":
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124 colused <- brewer.pal(ncolors, "$colorchoice.name")
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125 #elif $colorchoice.type == "two"
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126 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2"))(ncolors)
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127 #elif $colorchoice.type == "three"
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128 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2", "$colorchoice.color3"))(ncolors)
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129 #end if
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130
5
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131 #if $image_file_format == "pdf":
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132 pdf(file='$output1')
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133 #else:
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134 png(file='$output1', res=240, height=2000, width=2000)
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135 #end if
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136
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137 heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
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138 distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
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139 col=colused, trace="none", density.info = "none", margins=label_margins,
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140 main = '$title', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
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141 keysize=3, key.xlab='$key', key.title='', key.par=key_margins,
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142 lmat=layout_matrix, lhei=lheight, lwid=lwidth)
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143
0
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144 dev.off()
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145 ]]></configfile>
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146 </configfiles>
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147
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148 <inputs>
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149 <param name="input1" type="data" format="tabular"
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150 label="Input should have column headers - these will be the columns that are plotted and row names."/>
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151 <param name="title" type="text" format="txt" label="Plot title"/>
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152 <param name="key" type="text" format="txt" label="key title"/>
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153 <param name="transform" type="select" label="Data transformation">
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154 <option value="none" selected="true">Plot the data as it is</option>
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155 <option value="log2">Log2(value) transform my data</option>
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156 <option value="log2plus1">Log2(value+1) transform my data</option>
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157 <option value="log10">Log10(value) transform my data</option>
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158 <option value="log10plus1">Log10(value+1) transform my data</option>
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159 </param>
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160 <conditional name="zscore_cond">
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161 <param name="zscore" type="select" label="Compute z-scores prior to clustering">
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162 <option value="none" selected="true">Do not compute z-scores</option>
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163 <option value="rows">Compute on rows</option>
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164 <option value="cols">Compute on columns</option>
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165 </param>
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166 <when value="none">
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167 <param name="scale" type="select" label="Scale data on the plot (after clustering)" >
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168 <option value="none" selected="true">Do not scale my data</option>
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169 <option value="row">Scale my data by row</option>
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170 <option value="column">Scale my data by column</option>
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171 </param>
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172 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
173 <when value="rows"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
174 <when value="cols"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
175 </conditional>
4
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parents: 3
diff changeset
176 <conditional name="cluster_cond">
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
177 <param name="cluster" type="select" label="Enable data clustering">
7
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
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178 <option value="yes" selected="true">Yes</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
179 <option value="no">No</option>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
180 </param>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
181 <when value="yes">
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
182 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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183 <option value="both" selected="true">Cluster rows and columns</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
184 <option value="row">Cluster rows and not columns</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
185 <option value="column">Cluster columns and not rows</option>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
186 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
187 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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188 <option value="euclidean" selected="true">Euclidean</option>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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189 <option value="maximum">Maximum</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
190 <option value="manhattan">Manhattan</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
191 <option value="canberra">Canberra</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
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192 <option value="binary">Binary</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
193 <option value="minkowski">Minkowski</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
194 <option value="pearson_correlation">Pearson's correlation (1 - correlation coefficient)</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
195 <option value="spearmann_correlation">Spearmann's correlation (1 - correlation coefficient)</option>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
196 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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197 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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198 <option value="complete" selected="true">Complete</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
199 <option value="average">Average (= UPGMA)</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
200 <option value="ward.D">ward.D</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
201 <option value="ward.D2">ward.D2</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
202 <option value="single">single</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
203 <option value="mcquitty">mcquitty (= WPGMA)</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
204 <option value="median">median (= WPGMC)</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
205 <option value="centroid">centroid (= UPGMC)</option>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
206 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
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207 </when>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
208 <when value="no"/>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
209 </conditional>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
210 <param name="labels" type="select" label="Labeling columns and rows" >
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
211 <option value="both" selected="true">Label my columns and rows</option>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
212 <option value="rows">Label rows and not columns</option>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
213 <option value="columns">Label columns and not rows</option>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
214 <option value="none">Do not label rows or columns</option>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
215 </param>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
216 <conditional name="colorchoice">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
217 <param name="type" type="select" label="Type of colormap to use">
7
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
218 <option value="palettes" selected="true">RColorBrewer palettes</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
219 <option value="two">Gradient with 2 colors</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
220 <option value="three">Gradient with 3 colors</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
221 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
222 <when value="palettes">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
223 <param name="name" type="select" label="Name of the colormap">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
224 <option value="BrBG">BrBG</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
225 <option value="PiYG">PiYG</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
226 <option value="PRGn">PRGn</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
227 <option value="PuOr">PuOr</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
228 <option value="RdBu">RdBu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
229 <option value="RdGy">RdGy</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
230 <option value="RdYlBu">RdYlBu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
231 <option value="RdYlGn">RdYlGn</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
232 <option value="Spectral">Spectral</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
233 <option value="Blues">Blues</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
234 <option value="BuGn">BuGn</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
235 <option value="BuPu">BuPu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
236 <option value="GnBu">GnBu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
237 <option value="Greens">Greens</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
238 <option value="Greys">Greys</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
239 <option value="Oranges">Oranges</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
240 <option value="OrRd">OrRd</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
241 <option value="PuBu">PuBu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
242 <option value="PuBuGn">PuBuGn</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
243 <option value="PuRd">PuRd</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
244 <option value="Purples">Purples</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
245 <option value="RdPu">RdPu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
246 <option value="Reds">Reds</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
247 <option value="YlGn">YlGn</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
248 <option value="YlGnBu">YlGnBu</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
249 <option value="YlOrBr">YlOrBr</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
250 <option value="YlOrRd">YlOrRd</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
251 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
252 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
253 <when value="two">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
254 <param name="color1" type="color" value="#ffffff" label="First color" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
255 <param name="color2" type="color" value="#ff0000" label="Second color" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
256 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
257 <when value="three">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
258 <param name="color1" type="color" value="#0000ff" label="First color" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
259 <param name="color2" type="color" value="#ffffff" label="Second color" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
260 <param name="color3" type="color" value="#ff0000" label="Third color" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
261 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
262 </conditional>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
263 <param name="image_file_format" type="select" label="Output format">
7
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
264 <option value="pdf" selected="true">PDF</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
265 <option value="png">PNG</option>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
266 </param>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
267 </inputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
268 <outputs>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
269 <data name="output1" format="pdf">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
270 <change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
271 <when input="image_file_format" value="png" format="png" />
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
272 </change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
273 </data>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
274 </outputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
275 <tests>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
276 <test>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
277 <param name="input1" value="mtcars.txt"/>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
278 <param name="cluster" value="yes"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
279 <param name="type" value="two"/>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
280 <output name="output1" file="result1.pdf" compare="sim_size"/>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
281 </test>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
282 <test>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
283 <param name="input1" value="mtcars.txt"/>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
284 <param name="cluster" value="no"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
285 <param name="image_file_format" value="png"/>
8
374e9062d874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents: 7
diff changeset
286 <output name="output1" file="result2.png" compare="sim_size" delta="12000" />
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
287 </test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
288 <test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
289 <param name="input1" value="mtcars.txt"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
290 <param name="zscore" value="cols"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
291 <param name="cluster" value="yes"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
292 <param name="cluster_cols_rows" value="row"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
293 <param name="labels" value="rows"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
294 <param name="type" value="three"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
295 <param name="image_file_format" value="png"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
296 <output name="output1" file="result3.png" compare="sim_size"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
297 </test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
298 <test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
299 <param name="input1" value="mtcars.txt"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
300 <param name="cluster" value="yes"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
301 <param name="distance" value="pearson_correlation"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
302 <param name="type" value="two"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
303 <output name="output1" file="result1pearson.pdf" compare="sim_size"/>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
304 </test>
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
305 <test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
306 <param name="input1" value="mtcars.txt"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
307 <param name="zscore" value="rows"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
308 <param name="type" value="three"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
309 <param name="image_file_format" value="png"/>
8
374e9062d874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
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diff changeset
310 <output name="output1" file="result4.png" compare="sim_size" delta="12000" />
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
311 </test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
312 <test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
313 <param name="input1" value="mtcars.txt"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
314 <param name="cluster" value="yes"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
315 <param name="distance" value="pearson_correlation"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
316 <param name="scale" value="row"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
317 <param name="type" value="three"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
318 <param name="image_file_format" value="png"/>
8
374e9062d874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents: 7
diff changeset
319 <output name="output1" file="result5.png" compare="sim_size" delta="12000" />
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
320 </test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
321 <test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
322 <param name="input1" value="mtcars.txt"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
323 <param name="cluster" value="yes"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
324 <param name="distance" value="spearmann_correlation"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
325 <param name="scale" value="column"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
326 <param name="type" value="three"/>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
327 <param name="image_file_format" value="png"/>
8
374e9062d874 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
iuc
parents: 7
diff changeset
328 <output name="output1" file="result6.png" compare="sim_size" delta="12000" />
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
329 </test>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
330 </tests>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
331 <help><![CDATA[
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
332 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.
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
333
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
334 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.
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
335 ]]></help>
2
c6bfec911a41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 1
diff changeset
336 <citations>
7
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
337 <citation type="bibtex">
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
338 @ONLINE{heatmap2,
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
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diff changeset
339 title = {heatmap.2: Enhanced Heat Map},
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
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diff changeset
340 url = {https://rdocumentation.org/packages/gplots/versions/3.1.3/topics/heatmap.2}
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
341 }
53460afd5115 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 48958ce8d7a3b630dfcca78d12222ac67f1602fe
iuc
parents: 6
diff changeset
342 </citation>
2
c6bfec911a41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents: 1
diff changeset
343 </citations>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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344 </tool>