--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sc3-calc-consens.xml	Wed Apr 03 11:29:09 2019 -0400
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="sc3_calc_consens" name="SC3 Calculate Consensus" version="@TOOL_VERSION@+galaxy0">
+  <description>from multiple runs of k-means clustering</description>
+  <macros>
+    <import>sc3-macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+sc3-sc3-calc-consens.R -i '${sc3_kmeans}' -t '${clusters}' -o '${sc3_consensus}'
+  ]]></command>
+
+  <inputs>
+    <param name="sc3_kmeans" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with stored kmeans clustering"/>
+  </inputs>
+
+  <outputs>
+    <data name="clusters" format="csv" label="${tool.name} on ${on_string}: text table storing consensus clustering"/>
+    <data name="sc3_consensus" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment with consensus matrix."/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="sc3_kmeans" value="sc3_kmeans.rds"/>
+      <output name="clusters" value="consensus_clusters.txt"/>
+      <output name="sc3_consensus" file="sc3_consensus.rds"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+==============================================
+This function calculates consensus clustering.
+==============================================
+
+Calculate consensus matrices based on the clustering solutions contained in the
+kmeans item of the sc3 slot of the metadata(object). It then creates and
+populates the consensus item of the sc3 slot with consensus matrices, their
+hierarchical clusterings in hclust objects, and Silhouette indeces of the
+clusters. It also removes the previously calculated kmeans clusterings from the
+sc3 slot, as they are not needed for further analysis.
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>