Mercurial > repos > iuc > ggplot2_heatmap2

annotate heatmap2.xml @ 10:48b42ee61bc5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
author iuc
date Tue, 12 Nov 2024 16:44:40 +0000
parents 51c6ccaace7e
children
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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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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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48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
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4 <token name="@VERSION_SUFFIX@">1</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>
2
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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7 <requirement type="package" version="@TOOL_VERSION@">r-gplots</requirement>
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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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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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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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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"
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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
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56 srtCol <- 30
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57 #if $labels == "both"
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58 rlabs <- NULL
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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"
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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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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
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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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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48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
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82 # Layout is:
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
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83 # 4 = color key | 3 = dendrogram for columns
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
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84 # 2 = dendrogram for rows | 1 = heatmap
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85 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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86 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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87 lheight <- c(1, 5)
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88 lwidth <- c(1,3)
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89 #elif $cluster_cond.cluster_cols_rows == "row"
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90 reorder_cols <- FALSE
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91 reorder_rows <- TRUE
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92 # Layout is:
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93 # 3 = dendrogram for columns (not plotted) + title | 4 = color key
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94 # 2 = dendrogram for rows | 1 = heatmap
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95 layout_matrix <- rbind(c(3,4), c(2,1))
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96 key_margins <- list(mar=c(3,5,1,10))
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97 lheight <- c(1,7)
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98 lwidth <- c(1,3)
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99 #elif $cluster_cond.cluster_cols_rows == "column"
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100 reorder_cols <- TRUE
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101 reorder_rows <- FALSE
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102 # Layout is:
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103 # nothing | 4 = color key
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104 # nothing | 3 = dendrogram for columns
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105 # 2 = dendrogram for rows (not plotted) | 1 = heatmap
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106 layout_matrix <- rbind(c(0, 4), c(0, 3), c(2, 1))
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107 key_margins <- list(mar=c(1, 5, 1, 10))
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108 lheight <- c(0.5, 1, 5)
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109 lwidth <- c(0.01, 1)
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110 #end if
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111 hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
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112 #if $cluster_cond.distance == 'pearson_correlation':
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113 dist_fun <- function(x) as.dist(1 - cor(t(x)))
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114 #elif $cluster_cond.distance == 'spearmann_correlation':
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115 dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman"))
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116 #else:
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117 dist_fun <- function(x) dist(x, method='$cluster_cond.distance')
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118 #end if
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119 #else:
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120 dendrogramtoplot <- "none"
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121 reorder_cols <- FALSE
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122 reorder_rows <- FALSE
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123 layout_matrix <- rbind(c(0,4,3), c(0,1,2))
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124 key_margins <- list(mar=c(3,5,1,10))
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125 lheight <- c(1,7)
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126 lwidth <- c(1,7,1)
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127 hclust_fun <- hclust
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128 dist_fun <- dist
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129 label_margins <- c(8,2)
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130 #end if
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131
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132 ncolors <- 50
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133 #if $colorchoice.type == "palettes":
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134 colused <- brewer.pal(ncolors, "$colorchoice.name")
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135 #elif $colorchoice.type == "two"
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136 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2"))(ncolors)
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137 #elif $colorchoice.type == "three"
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138 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2", "$colorchoice.color3"))(ncolors)
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139 #end if
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140
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141 #if $image_file_format == "pdf":
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142 pdf(file='$output1')
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143 #else:
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144 png(file='$output1', res=240, height=2000, width=2000)
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145 #end if
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146
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147 heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
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148 distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
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149 col=colused, trace="none", density.info = "none", margins=label_margins,
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150 main = '$title', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
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151 keysize=3, key.xlab='$key', key.title='', key.par=key_margins,
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152 lmat=layout_matrix, lhei=lheight, lwid=lwidth)
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153
0
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154 dev.off()
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155 ]]></configfile>
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156 </configfiles>
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157
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158 <inputs>
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159 <param name="input1" type="data" format="tabular"
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160 label="Input should have column headers - these will be the columns that are plotted and row names."/>
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161 <param name="title" type="text" format="txt" label="Plot title"/>
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162 <param name="key" type="text" format="txt" label="key title"/>
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163 <param name="transform" type="select" label="Data transformation">
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164 <option value="none" selected="true">Plot the data as it is</option>
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165 <option value="log2">Log2(value) transform my data</option>
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166 <option value="log2plus1">Log2(value+1) transform my data</option>
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167 <option value="log10">Log10(value) transform my data</option>
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168 <option value="log10plus1">Log10(value+1) transform my data</option>
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169 </param>
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170 <conditional name="zscore_cond">
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171 <param name="zscore" type="select" label="Compute z-scores prior to clustering">
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172 <option value="none" selected="true">Do not compute z-scores</option>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
173 <option value="rows">Compute on rows</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
174 <option value="cols">Compute on columns</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
175 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
176 <when value="none">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
177 <param name="scale" type="select" label="Scale data on the plot (after clustering)" >
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
178 <option value="none" selected="true">Do not scale my data</option>
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="row">Scale my data by row</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
180 <option value="column">Scale my data by column</option>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
181 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
182 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
183 <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
184 <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
185 </conditional>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
186 <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
187 <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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188 <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
189 <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
190 </param>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
191 <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
192 <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
diff changeset
193 <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
194 <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
195 <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
196 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
197 <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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198 <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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199 <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
200 <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
201 <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
diff changeset
202 <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
203 <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
204 <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
205 <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
206 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
207 <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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208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
217 </when>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
218 <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
219 </conditional>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
220 <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
221 <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
222 <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
223 <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
224 <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
225 </param>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
226 <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
227 <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
228 <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
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229 <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
230 <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
231 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
232 <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
233 <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
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234 <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
235 <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
236 <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
237 <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
238 <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
239 <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
240 <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
241 <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
242 <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
243 <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
244 <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
245 <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
246 <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
247 <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
248 <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
249 <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
250 <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
251 <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
252 <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
253 <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
254 <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
255 <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
256 <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
257 <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
258 <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
259 <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
260 <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
261 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
262 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
263 <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
264 <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
265 <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
266 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
267 <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
268 <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
269 <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
270 <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
271 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
272 </conditional>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
273 <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
274 <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
275 <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
276 </param>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
277 </inputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
278 <outputs>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
279 <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
280 <change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
281 <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
282 </change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
283 </data>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
284 </outputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
285 <tests>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
286 <test>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
287 <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
288 <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
289 <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
290 <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
291 </test>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
292 <test>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
293 <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
294 <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
295 <param name="image_file_format" value="png"/>
10
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
296 <output name="output1" file="result2.png" compare="image_diff" />
5
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="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
301 <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
302 <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
303 <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
304 <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
305 <param name="image_file_format" value="png"/>
10
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
306 <output name="output1" file="result3.png" compare="image_diff"/>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
307 </test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
308 <test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
309 <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
310 <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
311 <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
312 <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
313 <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
parents:
diff changeset
314 </test>
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
315 <test>
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="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
317 <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
318 <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
319 <param name="image_file_format" value="png"/>
10
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
320 <output name="output1" file="result4.png" compare="image_diff" />
6
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 <test>
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="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
324 <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
325 <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
326 <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
327 <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
328 <param name="image_file_format" value="png"/>
10
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
329 <output name="output1" file="result5.png" compare="image_diff" />
6
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
330 </test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
331 <test>
566197475670 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit 4f9970932fa3521656d5618582ba5df4173ca66c"
iuc
parents: 5
diff changeset
332 <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
333 <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
334 <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
335 <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
336 <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
337 <param name="image_file_format" value="png"/>
10
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
338 <output name="output1" file="result6.png" compare="image_diff" />
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
339 </test>
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
340 <test>
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
341 <param name="input1" value="mtcars.txt"/>
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
diff changeset
342 <param name="cluster" value="yes"/>
48b42ee61bc5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e3d7e01c96e49e65000f45d07e453d9f2625651a
iuc
parents: 9
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343 <param name="cluster_cols_rows" value="column"/>
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344 <param name="distance" value="pearson_correlation"/>
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345 <param name="scale" value="row"/>
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346 <param name="type" value="palettes"/>
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347 <param name="name" value="YlOrBr"/>
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348 <param name="image_file_format" value="png"/>
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349 <output name="output1" file="result7.png" compare="image_diff" />
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350 </test>
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351 </tests>
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352 <help><![CDATA[
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353 This tool employs the heatmap.2 function from the R gplots package and will generate a heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance method and the Complete hierarchical clustering method by default.
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354
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355 Input data should have row labels in the first column and column labels. For example, the row labels (the first column) should represent gene IDs and the column labels should represent sample IDs.
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356 ]]></help>
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357 <citations>
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358 <citation type="bibtex">
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359 @ONLINE{heatmap2,
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360 title = {heatmap.2: Enhanced Heat Map},
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361 url = {https://rdocumentation.org/packages/gplots/versions/3.1.3/topics/heatmap.2}
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362 }
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363 </citation>
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364 </citations>
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365 </tool>