Mercurial > repos > iuc > ggplot2_heatmap2

annotate heatmap2.xml @ 5:3b37b1b1c3a7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
author iuc
date Tue, 12 Apr 2022 15:53:40 +0000
parents ca7cb0eaad62
children 566197475670
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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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1 <tool id="ggplot2_heatmap2" name="heatmap2" version="@VERSION@">
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2 <macros>
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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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3 <token name="@VERSION@">3.1.1</token>
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4 </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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5 <requirements>
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6 <requirement type="package" version="@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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7 <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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8 </requirements>
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9 <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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10 cat '$script' &&
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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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11 Rscript '$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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12 ]]></command>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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13 <configfiles>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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14 <configfile name="script"><![CDATA[
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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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15 ## Setup R error handling to go to stderr
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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16 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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17
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ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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18 ## Unify locale settings
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
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19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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21 ## Import library
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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22 library("RColorBrewer")
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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23 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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25 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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27 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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28 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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29
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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30 #if $transform == "none"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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31 linput <- mat_input
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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32 #elif $transform == "log2"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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33 linput <- log2(mat_input)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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34 #elif $transform == "log2plus1"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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35 linput <- log2(mat_input+1)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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36 #elif $transform == "log10"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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37 linput <- log10(mat_input)
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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38 #elif $transform == "log10plus1"
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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39 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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40 #end if
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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41
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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42 #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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43 linput <- t(apply(linput, 1, scale))
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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44 colnames(linput) <- colnames(input)
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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45 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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46 scale <- "none"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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47 #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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48 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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49 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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50 scale <- "none"
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51 #elif $zscore_cond.zscore == "none":
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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52 scale <- "$zscore_cond.scale"
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53 #end if
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54
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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55 srtCol <- 45
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56 #if $labels == "both"
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57 rlabs <- NULL
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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58 clabs <- NULL
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59 #elif $labels == "rows"
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60 rlabs <- NULL
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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61 clabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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62 srtCol <- NULL
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63 #elif $labels == "columns"
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64 rlabs <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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65 clabs <- NULL
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66 #elif $labels == "none"
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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 <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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69 srtCol <- NULL
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70 #end if
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71
5
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72 #if $cluster_cond.cluster == "yes":
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73 dendrogramtoplot <- "$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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74 #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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75 reorder_cols <- TRUE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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76 reorder_rows <- TRUE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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77 #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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78 reorder_cols <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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79 reorder_rows <- TRUE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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80 #elif $cluster_cond.cluster_cols_rows == "column"
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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81 reorder_cols <- TRUE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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82 reorder_rows <- FALSE
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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83 #end if
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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84 hclust_fun <- function(x) hclust(x, method='$cluster_cond.clustering')
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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85 #if $cluster_cond.distance == 'pearson_correlation':
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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86 dist_fun <- function(x) as.dist(1 - cor(t(x)))
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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87 #elif $cluster_cond.distance == 'spearmann_correlation':
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88 dist_fun <- function(x) as.dist(1 - cor(t(x), method="spearman"))
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89 #else:
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90 dist_fun <- function(x) dist(x, method='$cluster_cond.distance')
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91 #end if
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92 #else:
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93 dendrogramtoplot <- "none"
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94 reorder_cols <- FALSE
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95 reorder_rows <- FALSE
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96 hclust_fun <- hclust
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97 dist_fun <- dist
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98 #end if
0
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99
5
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100 ncolors <- 50
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101 #if $colorchoice.type == "palettes":
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102 colused <- brewer.pal(ncolors, "$colorchoice.name")
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103 #elif $colorchoice.type == "two"
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104 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2"))(ncolors)
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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105 #elif $colorchoice.type == "three"
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106 colused <- colorRampPalette(c("$colorchoice.color1", "$colorchoice.color2", "$colorchoice.color3"))(ncolors)
0
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107 #end if
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108
5
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109 #if $image_file_format == "pdf":
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110 pdf(file='$output1')
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111 #else:
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112 png(file='$output1')
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113 #end if
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114
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115 heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
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116 distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
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117 col=colused, trace="none", density.info = "none", margins=c(8,8),
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118 main = '$title', key.xlab='$key', keysize=1, cexCol=0.8, cexRow = 0.8, srtCol=srtCol)
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119
0
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120 dev.off()
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121 ]]></configfile>
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122 </configfiles>
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123
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124 <inputs>
5
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125 <param name="input1" type="data" format="tabular"
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126 label="Input should have column headers - these will be the columns that are plotted and row names."/>
4
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127 <param name="title" type="text" format="txt" label="Plot title"/>
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128 <param name="key" type="text" format="txt" label="key title"/>
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129 <param name="transform" type="select" label="Data transformation">
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130 <option value="none">Plot the data as it is</option>
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131 <option value="log2">Log2(value) transform my data</option>
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132 <option value="log2plus1">Log2(value+1) transform my data</option>
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133 <option value="log10">Log10(value) transform my data</option>
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134 <option value="log10plus1">Log10(value+1) transform my data</option>
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135 </param>
5
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136 <conditional name="zscore_cond">
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137 <param name="zscore" type="select" label="Compute z-scores prior to clustering">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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138 <option value="none">Do not compute z-scores</option>
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139 <option value="rows">Compute on rows</option>
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140 <option value="cols">Compute on columns</option>
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141 </param>
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142 <when value="none">
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143 <param name="scale" type="select" label="Scale data on the plot (after clustering)" >
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144 <option value="none" selected="true">Do not scale my data</option>
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145 <option value="row">Scale my data by row</option>
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146 <option value="column">Scale my data by column</option>
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147 </param>
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148 </when>
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149 <when value="rows"/>
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150 <when value="cols"/>
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151 </conditional>
4
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152 <conditional name="cluster_cond">
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153 <param name="cluster" type="select" label="Enable data clustering">
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154 <option value="yes">Yes</option>
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155 <option value="no">No</option>
4
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156 </param>
5
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157 <when value="yes">
4
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158 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
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159 <option value="both" selected="true">Cluster rows and columns</option>
5
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160 <option value="row">Cluster rows and not columns</option>
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161 <option value="column">Cluster columns and not rows</option>
4
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162 </param>
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163 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
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164 <option value="euclidean" selected="true">Euclidean</option>
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165 <option value="maximum">Maximum</option>
5
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166 <option value="manhattan">Manhattan</option>
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167 <option value="canberra">Canberra</option>
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168 <option value="binary">Binary</option>
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169 <option value="minkowski">Minkowski</option>
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170 <option value="pearson_correlation">Pearson's correlation (1 - correlation coefficient)</option>
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171 <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
172 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
173 <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
diff changeset
174 <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
175 <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
176 <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
177 <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
178 <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
179 <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
180 <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
181 <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
182 </param>
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
183 </when>
5
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="no"/>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
parents: 3
diff changeset
185 </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
186 <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
187 <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
188 <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
189 <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
190 <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
191 </param>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
192 <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
193 <param name="type" type="select" label="Type of colormap to use">
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="palettes">RColorBrewer palettes</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="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
196 <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
197 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
198 <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
199 <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
200 <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
201 <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
202 <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
203 <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
204 <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
205 <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
206 <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
207 <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
208 <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
209 <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
210 <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
211 <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
212 <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
213 <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
214 <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
215 <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
216 <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
217 <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
218 <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
219 <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
220 <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
221 <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
222 <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
223 <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
224 <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
225 <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
226 <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
227 </param>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
228 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
229 <when value="two">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
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230 <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
231 <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
232 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
233 <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
234 <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
235 <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
236 <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
237 </when>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
238 </conditional>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
239 <param name="image_file_format" type="select" label="Output format">
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
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240 <option value="pdf">PDF</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="png">PNG</option>
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
242 </param>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
243 </inputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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244 <outputs>
5
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
245 <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
246 <change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
247 <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
248 </change_format>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
iuc
parents: 4
diff changeset
249 </data>
0
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
250 </outputs>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
251 <tests>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff changeset
252 <test>
76380bf74511 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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diff changeset
253 <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
254 <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
255 <param name="type" value="two"/>
4
ca7cb0eaad62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit e7b5919a8e06595b23e8fc31b975fc508f5081b3
iuc
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256 <output name="output1" file="result1.pdf" compare="sim_size"/>
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257 </test>
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258 <test>
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259 <param name="input1" value="mtcars.txt"/>
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260 <param name="cluster" value="no"/>
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261 <param name="image_file_format" value="png"/>
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262 <output name="output1" file="result2.png" compare="sim_size"/>
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263 </test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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264 <test>
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265 <param name="input1" value="mtcars.txt"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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266 <param name="zscore" value="cols"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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267 <param name="cluster" value="yes"/>
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268 <param name="cluster_cols_rows" value="row"/>
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269 <param name="labels" value="rows"/>
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270 <param name="type" value="three"/>
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271 <param name="image_file_format" value="png"/>
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272 <output name="output1" file="result3.png" compare="sim_size"/>
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273 </test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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274 <test>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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275 <param name="input1" value="mtcars.txt"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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276 <param name="cluster" value="yes"/>
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277 <param name="distance" value="pearson_correlation"/>
3b37b1b1c3a7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2 commit b04b237daba99e6992b27d1b65524744feb07d7d"
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278 <param name="type" value="two"/>
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279 <output name="output1" file="result1pearson.pdf" compare="sim_size"/>
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280 </test>
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281 </tests>
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282 <help><![CDATA[
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283 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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284
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285 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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286 ]]></help>
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287 <citations>
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288 </citations>
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289 </tool>