--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seurat_run_tsne.xml	Wed Apr 03 11:19:13 2019 -0400
@@ -0,0 +1,84 @@
+<tool id="seurat_run_tsne" name="Seurat RunTSNE" version="2.3.1+galaxy1">
+    <description>run t-SNE dimensionality reduction</description>
+    <macros>
+        <import>seurat_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version" />
+    <command detect_errors="exit_code"><![CDATA[
+seurat-run-tsne.R
+
+--input-object-file '$input'
+
+#if $genes_use:
+  --genes-use '$genes_use'
+#end if
+
+#if str($adv.dims_use):
+    --dims-use \$(seq -s , 1 '$adv.dims_use')
+#else
+    --dims-use 1,10
+#end if
+
+#if not $adv.do_fast:
+    --do-fast '$adv.do_fast'
+#end if
+
+--output-object-file '$output'
+--output-embeddings-file output_embed
+]]></command>
+
+    <inputs>
+        <param name="input" argument="--input-obj-file" type="data" format="rdata" label="Seurat RDS object" help="The RDS/Rdata result of Seurat FindClusters."/>
+        <expand macro="genes-use-input"/>
+        <section name="adv" title="Advanced Options">
+            <expand macro="dims-use-input"/>
+            <param name="do_fast" label="Faster execution" argument="--do-fast" checked="true" type="boolean" truevalue="" falsevalue="FALSE" help="If TRUE, uses the Barnes-hut implementation, which runs faster, but is less flexible. TRUE by default."/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" ftype="rdata" value="out_findclust.rds"/>
+            <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
+It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
+interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
+types of single cell data.
+
+Run t-SNE dimensionality reduction on selected features. Has the option of
+running in a reduced dimensional space (i.e. spectral tSNE, recommended),
+or running based on a set of genes. For details about stored TSNE calculation
+parameters, see standard output of the tool.
+
+-----
+
+**Inputs**
+
+    * RDS object
+
+-----
+
+**Outputs**
+
+    * Seurat RDS object
+
+.. _Seurat: https://www.nature.com/articles/nbt.4096
+.. _Satija Lab: https://satijalab.org/seurat/
+
+@VERSION_HISTORY@
+]]></help>
+      <expand macro="citations" />
+</tool>