--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sc3-calc-biology.xml	Wed Apr 03 11:32:26 2019 -0400
@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="sc3_calc_biology" name="SC3 DiffExp" version="@TOOL_VERSION@+galaxy1">
+  <description>calculates DE genes, marker genes and cell outliers</description>
+  <macros>
+    <import>sc3-macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+sc3-sc3-calc-biology.R -i '${sc3_consensus}' -o '${sc3_biology_markers}' -t '${sc3_biology_markers_tsv}' -k '${ks}' -r '${regime}'
+  ]]></command>
+
+  <inputs>
+    <param name="sc3_consensus" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with stored consensus kmeans clustering"/>
+
+    <param name="ks" argument="--ks" type="text" label="An integer or comma-separated list of integers">
+      <validator type="regex" message="Please only enter integers or comma-separated list of integers">^[0-9]+(,[0-9]+)*$</validator>
+    </param>
+
+    <param name="regime" argument="--regime" type="select" label="Biological analysis to perform">
+      <option value="marker" selected="true">Marker gene identification</option>
+      <option value="de">Differential expression</option>
+      <option value="outl">Outlier identification</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="sc3_biology_markers" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment storing the DE markers"/>
+    <data name="sc3_biology_markers_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv table storing the DE markers"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="sc3_consensus" value="sc3_consensus.rds"/>
+      <param name="ks" value="7,8"/>
+      <param name="regime" value="marker"/>
+      <output name="sc3_biology_markers" file="sc3_bio_sce.rds"/>
+      <output name="sc3_biology_markers_tsv" file="sc3_biology_markers.tsv"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+========================================================
+This function performs differential expression analysis.
+========================================================
+
+Calculate differentially expressed (DE) genes, marker genes and cell outliers
+based on the consensus SC3 clusterings.
+
+@HELP@
+
+@VERSION_HISTORY@
+  ]]></help>
+  <expand macro="citations" />
+</tool>