--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rtsne.xml	Tue Aug 22 07:38:53 2017 -0400
@@ -0,0 +1,122 @@
+<tool id="tsne" name="rtsne" version="0.0.2">
+    <requirements>
+        <requirement type="package">r-getopt</requirement>
+        <requirement type="package">r-rtsne</requirement>
+        <requirement type="package">r-ggplot2</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+cat '$script' &&
+Rscript '$script' &&
+mv output_plot.pdf $output1
+    ]]></command>
+    <configfiles>
+        <configfile name="script"><![CDATA[
+## Setup R error handling to go to stderr
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+## Import library
+library(Rtsne)
+library(ggplot2)
+
+all <- read.delim('$input1', sep='\t', header=TRUE)
+
+data = $data
+name = $name
+
+#if $transform == "none"
+    log.all <- all[, data:ncol(all)]
+#elif $transform == "log2"
+    log.all <- log2(all[, data:ncol(all)])
+#elsif $transform == "log2plus1"
+    log.all <- log2(1+all[, data:ncol(all)])
+#elif $transform == "log10"
+    log.all <- log(all[, data:ncol(all)])
+#elif $transform == "log10plus1"
+    log.all <- log(1+all[, data:ncol(all)])
+#end if
+
+## Show/hide legend
+#if $legend == "yes"
+    gg_legend = NULL
+#else
+    gg_legend = theme(legend.position="none")
+#end if
+
+set.seed($seed) ## Sets seed for reproducibility
+tsne_out <- Rtsne(as.matrix(log.all[,1:ncol(log.all)]), perplexity=$perp, theta=$theta) ## Run TSNE
+
+embedding <- as.data.frame(tsne_out\$Y)
+embedding\$Class <- as.factor(sub("Class_", "", all[,name]))
+
+ggplot(embedding, aes(x=V1, y=V2, color=Class)) +
+     geom_point(size=1.25) + 
+     gg_legend +
+     xlab("") +
+     ylab("") +
+     ggtitle('$title')
+
+ggsave(file='output_plot.pdf')
+dev.off()
+
+        ]]></configfile>
+    </configfiles>
+
+    <inputs>
+        <param name="input1" type="data" format="tabular"
+            label="Tabular input dataset"
+            help="Input should have column headers with an identifier column followed by consencutive numerical columns used for clustering"/>
+        <param name="title" type="text" format="txt" label="Plot title"/> 
+        <param name="seed" value="42.0" type="float" label="Seed value for reproducibiity" help="Set to 42 as default" />
+        <param name="perp" value="10.0" type="float" label="perplexity"/> 
+        <param name="theta" value="1.0" type="float" label="theta"/> 
+        <param name="name" value="1" type="data_column" data_ref="input1"
+            label="The column with the ID to use in grouping (or just an ID if plotting invdividuals)"/> 
+        <param name="data" value="2" type="data_column" data_ref="input1"
+            label="The column that contains the first numerical data"/> 
+        <param name="transform" type="select" label="Advanced - log transformation">
+            <option value="none">Plot the data as it is</option>
+            <option value="log2">Log2(value) transform my data</option>
+            <option value="log2plus1">Log2(value+1) transform my data</option>
+            <option value="log10">Log10(value) transform my data</option>
+            <option value="log10plus1">Log10(value+1) transform my data</option>
+        </param>
+
+        <param name="legend" type="select" label="Legend options">
+            <option value="yes">Include legend on plot</option>
+            <option value="no">Hide legend</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="mtcars.txt"/>
+            <param name="transform" value="none"/>
+            <param name="perp" value="10.0"/>
+            <output name="output1" file="Rplot.pdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten (see <https://github.com/lvdmaaten/bhtsne/>
+for more information on the original implementation).
+
+Your data should be in tabular format. Objects in rows will be clustered according to the observations in columns.
+Labels for objects can be assigned in the tool form by providing the column number of the identifier you wish to use.
+Additionaly, the first column containing numeric data should be provided to the tool form. 
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@Manual{,
+    title = {{Rtsne}: T-Distributed Stochastic Neighbor Embedding using
+      Barnes-Hut Implementation},
+    author = {Jesse H. Krijthe},
+    year = {2015},
+    note = {R package version 0.13},
+    url = {https://github.com/jkrijthe/Rtsne},
+  }
+        </citation>
+    </citations>
+</tool>