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annotate heatmap.xml @ 3:cf72f579d100 draft default tip

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap commit c035a5f14cb65f7020d51610fb16ec76dcae8aba
author artbio
date Sun, 10 Dec 2023 23:18:16 +0000
parents 17f627ee8f5a
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cf72f579d100 planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap commit c035a5f14cb65f7020d51610fb16ec76dcae8aba
artbio
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1 <tool id="high_dim_heatmap" name="Plot heatmap" version="3.1.3+galaxy0">
0
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2 <description>with high number of rows</description>
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3 <requirements>
3
cf72f579d100 planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap commit c035a5f14cb65f7020d51610fb16ec76dcae8aba
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4 <requirement type="package" version="3.1.3">r-gplots</requirement>
cf72f579d100 planemo upload for repository https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap commit c035a5f14cb65f7020d51610fb16ec76dcae8aba
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5 <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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8 cat '$script' &&
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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9 Rscript '$script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="script"><![CDATA[
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13 ## Setup R error handling to go to stderr
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14 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
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15
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16 ## Unify locale settings
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17 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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18
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19 ## Import library
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20 library("RColorBrewer")
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21 library("gplots")
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23 input <- read.delim('$input1', sep='\t', header=TRUE)
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24
2
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25 mat_input <- data.matrix(input[, 2:ncol(input)])
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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26 rownames(mat_input) <- input[, 1]
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22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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27
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28 #if $transform == "none"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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29 linput <- mat_input
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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30 #elif $transform == "log2"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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31 linput <- log2(mat_input)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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32 #elif $transform == "log2plus1"
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17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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33 linput <- log2(mat_input + 1)
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22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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34 #elif $transform == "log10"
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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35 linput <- log10(mat_input)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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36 #elif $transform == "log10plus1"
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37 linput <- log10(mat_input + 1)
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38 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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39
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40 #if $colorscheme == "whrd"
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41 colfunc <- colorRampPalette(c("white", "red"))
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22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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42 #elif $colorscheme == "whblu"
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43 colfunc <- colorRampPalette(c("white", "blue"))
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44 #elif $colorscheme == "blwhre"
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45 colfunc <- colorRampPalette(c("blue","white", "red"))
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46 #elif $colorscheme == "yeblu"
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47 colfunc <- colorRampPalette(c("lightyellow", "royalblue4"))
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48 #end if
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49
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50 #if $labels== "both"
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51 rlabs = NULL
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52 clabs = NULL
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53 #elif $labels== "rows"
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54 rlabs = NULL
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55 clabs = FALSE
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56 #elif $labels== "columns"
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57 rlabs = FALSE
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58 clabs = NULL
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59 #elif $labels== "none"
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60 rlabs = FALSE
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61 clabs = FALSE
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62 #end if
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63
2
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64 pdf(file = '$output1', paper = 'special', height = $height)
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65 par(cex.main = $title_size)
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66
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67 #if $cluster_cond.cluster:
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68 hclust_fun = function(x) hclust(x, method = '$cluster_cond.clustering')
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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69 dist_fun = function(x) dist(x, method = '$cluster_cond.distance')
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70 #if $cluster_cond.cluster_cols_rows == "rows":
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71 heatmap.2(linput, dendrogram="row", Colv = FALSE, Rowv = TRUE,
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72 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
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73 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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74 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
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75 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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76 #elif $cluster_cond.cluster_cols_rows == "columns":
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77 heatmap.2(linput, dendrogram = "column", Colv = TRUE, Rowv = FALSE,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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78 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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79 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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80 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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81 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
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82 #else
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83 heatmap.2(linput,
2
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84 distfun = dist_fun, hclustfun = hclust_fun, scale = '$scale', labRow = rlabs,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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85 labCol = clabs, col = colfunc(50), trace = "none", density.info = "none",
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
diff changeset
86 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
diff changeset
87 cexCol = 0.8, cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
88 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
89 #else
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
90 heatmap.2(linput,
2
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
diff changeset
91 dendrogram = "none", Colv = FALSE, Rowv = FALSE, scale = '$scale', labRow = rlabs,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
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92 labCol = clabs, col = colfunc(50), trace="none", density.info = "none",
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
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93 margins = c(8,8), main = '$title', key.xlab = '$key', keysize = 1, cexCol = 0.8,
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
parents: 1
diff changeset
94 cexRow = $rowfontsize, srtCol = 45, lhei = c(1, $lineheight))
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
95 #end if
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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96
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
97 dev.off()
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
98 ]]></configfile>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
99 </configfiles>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
100
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
101 <inputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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102 <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
103 <param name="title" type="text" format="txt" label="Plot title"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
104 <param name="key" type="text" format="txt" label="key title"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
105 <param name="transform" type="select" label="Data transformation">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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106 <option value="none">Plot the data as it is</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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107 <option value="log2">Log2(value) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
108 <option value="log2plus1">Log2(value+1) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
109 <option value="log10">Log10(value) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
110 <option value="log10plus1">Log10(value+1) transform my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
111 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
112 <conditional name="cluster_cond">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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113 <param name="cluster" type="select" label="Enable data clustering">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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114 <option value="true">Yes</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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115 <option value="">No</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
116 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
117 <when value="true">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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118 <param name="cluster_cols_rows" type="select" label="Clustering columns and rows">
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
119 <option value="both" selected="true">Cluster rows and columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
120 <option value="rows">Cluster rows and not columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
121 <option value="columns">Cluster columns and not rows</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
122 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
123 <param name="distance" type="select" label="Distance method" help="The method used to compute the distance (dissimilarity) between both rows and columns. Default: Euclidean" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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124 <option value="euclidean" selected="true">Euclidean</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
125 <option value="maximum">Maximum</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
126 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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127 <param name="clustering" type="select" label="Clustering method" help="The method used to compute the hierarchical clustering. Default: Complete" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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128 <option value="complete" selected="true">Complete</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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129 <option value="average">Average</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
130 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
131 </when>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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132 <when value=""/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
133 </conditional>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
134 <param name="labels" type="select" label="Labeling columns and rows" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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135 <option value="both" selected="true">Label my columns and rows</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
136 <option value="rows">Label rows and not columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
137 <option value="columns">Label columns and not rows</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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138 <option value="none">Do not label rows or columns</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
139 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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140 <param name="colorscheme" type="select" label="Coloring groups" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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141 <option value="whrd" selected="true">White to red</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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142 <option value="whblu">White to blue</option>
1
58b36ae7baca "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 7c990ad7024035342c4abd6e3fa8feb1b2f2ac2c"
artbio
parents: 0
diff changeset
143 <option value="yeblu">Yellow to blue</option>
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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144 <option value="blwhre">Blue to white to red</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
145 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
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146 <param name="scale" type="select" label="Data scaling" >
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
147 <option value="none" selected="true">Do not scale my data</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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148 <option value="row">Scale my data by row</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
149 <option value="column">Scale my data by column</option>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
150 </param>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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151
2
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
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152 <param name="title_size" type="float" label="tweak main title size" value="1" />
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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153 <param name="height" type="float" label="tweak plot height" value="7" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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154 <param name="rowfontsize" type="float" label="tweak row label size" value="0.8" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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155 <param name="lineheight" type="integer" label="tweak line height" value="4" />
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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diff changeset
156 </inputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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157 <outputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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158 <data name="output1" format="pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
159 </outputs>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
parents:
diff changeset
160 <tests>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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161 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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162 <param name="input1" value="mtcars.txt"/>
2
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
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163 <param name="title" value="This is a pretty long title"/>
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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164 <param name="cluster" value="true"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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165 <output name="output1" file="result1.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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166 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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167 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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168 <param name="input1" value="mtcars.txt"/>
2
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
artbio
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169 <param name="title" value="This is a pretty long title"/>
0
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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170 <param name="cluster" value=""/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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171 <output name="output1" file="result2.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
artbio
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172 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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173 <test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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174 <param name="input1" value="complex_table.tsv"/>
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17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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175 <param name="title" value="This is a pretty long title for a complex plot"/>
17f627ee8f5a "planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit ba6089071a53fbf08df00c0f94dfc8515b7c858b"
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176 <param name="title_size" value="0.7"/>
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22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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177 <param name="transform" value="log2plus1"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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178 <param name="cluster" value=""/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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179 <param name="colorscheme" value="blwhre"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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180 <param name="height" value="21"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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181 <param name="rowfontsize" value="0.4"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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182 <param name="lineheight" value="15"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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183 <output name="output1" file="complex_result1.pdf"/>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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184 </test>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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185 </tests>
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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186 <help><![CDATA[
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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187 This tool employs the heatmap.2 function from the R gplots package and will generate a
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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188 heatmap of your data. If clustering is enabled, the heatmap uses the Euclidean distance
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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189 method and the Complete hierarchical clustering method by default.
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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190
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191 Input data should have row labels in the first column and column labels. For example,
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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192 the row labels (the first column) should represent gene IDs and the column labels should
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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193 represent sample IDs.
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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194
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195 To adapt heatmap.2 to high number of lines, tweak the parameters:
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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196
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197 - `tweak plot height`. By default 7 (inches), this can be increased to 14, 21, 28, etc..
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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198 - `tweak row label size`. By default 0.8. This is usually diminished to 0.3, 0.1, etc to
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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199 adapt the label font to high number of rows
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200 - `tweak line height`. By default 4. This is a metric to define the relative size of the
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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201 heatmap panel in the plot layout. This is a bit tricky to adjust, but should be adapted
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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202 when plot height is increased (typically to 8, 10, 15, etc...)
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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203
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204 For instance, upload the dataset
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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205 https://raw.githubusercontent.com/ARTbio/tools-artbio/master/tools/high_dim_heatmap/test-data/complex_table.tsv
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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206 to your account and test this tools with:
22d5d811dc37 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/high_dim_heatmap commit 3839913fd15008dd999f2da10dcb6797ddb8dbdc
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207
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208 - `tweak plot height` : 21.0
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209 - `tweak row label size`: 0.4
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210 - `tweak line height`: 14
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211
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212
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213 ]]></help>
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214 <citations>
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215 </citations>
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216 </tool>