--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raceid_inspectclusters.xml	Thu Nov 22 04:45:41 2018 -0500
@@ -0,0 +1,71 @@
+<tool id="raceid_inspectclusters" name="Cluster Inspection using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+    <description>examines gene expression within clusters</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_inspectclusters.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command><![CDATA[
+Rscript '$__tool_directory__/scripts/clusterinspect.R' @GET_VERSION@
+]]></version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+#set bin = 'clusterinspect.R'
+Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
+    ]]></command>
+  
+    <configfiles>
+        <configfile name="userconf" ><![CDATA[
+@STRING2VECTOR@
+
+@INSPECTCLUSTERS_CHEETAH@
+]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="inspectclusters_inputs" />
+    </inputs>
+
+    <outputs>
+        <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
+        <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
+            <filter>use_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <expand macro="inspectclusters_tests" />
+    </tests>
+    <help><![CDATA[
+
+RaceID3
+=========
+
+RaceID is a clustering algorithm for the identification of cell types from single-cell RNA-sequencing data. It was specifically designed for the detection of rare cells which correspond to outliers in conventional clustering methods.
+
+This module inspects the clusters generated from the previous clustering step (and requires the output RData file from it as input).
+
+The tool offers three modes of inspection which can all be activated at the same time, resulting in a single PDF report:
+
+ * Plot All Clusters:
+   * Produces a tSNE of all clusters, as well as a force-directed Fruchterman-Reingold (F-R) layout which may have tidier plots.
+ * Perform Subset Analysis:
+   * tSNE and F-R plots with cells whose name match the specified regex highlighted
+   
+ * Examine Genes of Interest:
+   * Expression plots highlighting a gene or genes of interest across all clusters
+
+ * Differential Gene Testing: 
+   * Examining the expression between 
+
+ * A list of the most differentially expressed genes in each cluster
+ * An output PDF that provides heatmaps for:
+    * The initial and final clustering (as determined using random forest)
+    * Heatmaps for each of the most differentially expressed genes in each cluster
+
+The tool requires the RData input from the previous filtering / normalisation / confounder removal step to work.
+
+
+
+]]></help>
+    <expand macro="citations" />
+</tool>