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annotate rtsne.xml @ 0:dd53658a0843 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
author iuc
date Tue, 22 Aug 2017 07:38:53 -0400
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children 53cfe6f313b3
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dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
iuc
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1 <tool id="tsne" name="rtsne" version="0.0.2">
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
iuc
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2 <requirements>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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3 <requirement type="package">r-getopt</requirement>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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4 <requirement type="package">r-rtsne</requirement>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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5 <requirement type="package">r-ggplot2</requirement>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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6 </requirements>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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7 <command detect_errors="exit_code"><![CDATA[
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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8 cat '$script' &&
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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9 Rscript '$script' &&
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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10 mv output_plot.pdf $output1
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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11 ]]></command>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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12 <configfiles>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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13 <configfile name="script"><![CDATA[
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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14 ## Setup R error handling to go to stderr
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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15 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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16 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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17
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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18 ## Import library
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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19 library(Rtsne)
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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20 library(ggplot2)
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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21
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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22 all <- read.delim('$input1', sep='\t', header=TRUE)
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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23
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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24 data = $data
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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25 name = $name
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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26
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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27 #if $transform == "none"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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28 log.all <- all[, data:ncol(all)]
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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29 #elif $transform == "log2"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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30 log.all <- log2(all[, data:ncol(all)])
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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31 #elsif $transform == "log2plus1"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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32 log.all <- log2(1+all[, data:ncol(all)])
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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33 #elif $transform == "log10"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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34 log.all <- log(all[, data:ncol(all)])
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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35 #elif $transform == "log10plus1"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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36 log.all <- log(1+all[, data:ncol(all)])
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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37 #end if
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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38
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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39 ## Show/hide legend
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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40 #if $legend == "yes"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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41 gg_legend = NULL
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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42 #else
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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43 gg_legend = theme(legend.position="none")
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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44 #end if
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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45
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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46 set.seed($seed) ## Sets seed for reproducibility
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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47 tsne_out <- Rtsne(as.matrix(log.all[,1:ncol(log.all)]), perplexity=$perp, theta=$theta) ## Run TSNE
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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48
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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49 embedding <- as.data.frame(tsne_out\$Y)
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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50 embedding\$Class <- as.factor(sub("Class_", "", all[,name]))
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51
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52 ggplot(embedding, aes(x=V1, y=V2, color=Class)) +
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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53 geom_point(size=1.25) +
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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54 gg_legend +
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55 xlab("") +
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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56 ylab("") +
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57 ggtitle('$title')
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58
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59 ggsave(file='output_plot.pdf')
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60 dev.off()
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61
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62 ]]></configfile>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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63 </configfiles>
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64
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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65 <inputs>
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66 <param name="input1" type="data" format="tabular"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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67 label="Tabular input dataset"
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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68 help="Input should have column headers with an identifier column followed by consencutive numerical columns used for clustering"/>
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69 <param name="title" type="text" format="txt" label="Plot title"/>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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70 <param name="seed" value="42.0" type="float" label="Seed value for reproducibiity" help="Set to 42 as default" />
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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71 <param name="perp" value="10.0" type="float" label="perplexity"/>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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72 <param name="theta" value="1.0" type="float" label="theta"/>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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73 <param name="name" value="1" type="data_column" data_ref="input1"
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74 label="The column with the ID to use in grouping (or just an ID if plotting invdividuals)"/>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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75 <param name="data" value="2" type="data_column" data_ref="input1"
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76 label="The column that contains the first numerical data"/>
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77 <param name="transform" type="select" label="Advanced - log transformation">
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78 <option value="none">Plot the data as it is</option>
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79 <option value="log2">Log2(value) transform my data</option>
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80 <option value="log2plus1">Log2(value+1) transform my data</option>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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81 <option value="log10">Log10(value) transform my data</option>
dd53658a0843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne commit 62172bde663955b6c3cb86dc22c47739824f014a
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82 <option value="log10plus1">Log10(value+1) transform my data</option>
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83 </param>
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84
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85 <param name="legend" type="select" label="Legend options">
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86 <option value="yes">Include legend on plot</option>
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87 <option value="no">Hide legend</option>
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88 </param>
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89 </inputs>
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90 <outputs>
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91 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="input1" value="mtcars.txt"/>
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96 <param name="transform" value="none"/>
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97 <param name="perp" value="10.0"/>
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98 <output name="output1" file="Rplot.pdf"/>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102 T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see <https://github.com/lvdmaaten/bhtsne/>
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103 for more information on the original implementation).
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104
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105 Your data should be in tabular format. Objects in rows will be clustered according to the observations in columns.
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106 Labels for objects can be assigned in the tool form by providing the column number of the identifier you wish to use.
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107 Additionaly, the first column containing numeric data should be provided to the tool form.
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108
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109 ]]></help>
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110 <citations>
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111 <citation type="bibtex">
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112 @Manual{,
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113 title = {{Rtsne}: T-Distributed Stochastic Neighbor Embedding using
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114 Barnes-Hut Implementation},
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115 author = {Jesse H. Krijthe},
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116 year = {2015},
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117 note = {R package version 0.13},
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118 url = {https://github.com/jkrijthe/Rtsne},
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119 }
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120 </citation>
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121 </citations>
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122 </tool>