--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hierarchical_clustering_heatmap.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,81 @@
+<tool id="secimtools_hierarchical_clustering_heatmap" name="Hierarchical Clustering Heatmap" version="@WRAPPER_VERSION@">
+    <description>- Calculate means per group and plot a heatmap.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+hierarchical_clustering_heatmap.py
+--input $input
+--design $design
+--uniqID $uniqID
+#if $dendogram
+    --dendogram
+#end if
+--labels $labels
+--fig $fig
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
+        <param name="dendogram" type="boolean" value="False" label="Add dendogram on heatmap" help="Select 'Yes' to print a dendogram over the heatmap."/>
+        <param name="labels" type="select" label="Select to remove labels from plots" multiple="true" display="checkboxes">
+            <option value="x">X-axis labels</option>
+            <option value="y">Y-axis labels</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="fig" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"     value="ST000006_data.tsv"/>
+            <param name="design"    value="ST000006_design.tsv"/>
+            <param name="uniqID"    value="Retention_Index" />
+            <param name="dendogram" value="True" />
+            <param name="labels"    value="x,y" />
+            <output name="fig"      file="ST000006_hierarchical_clustering_heatmap_figure.pdf" compare="sim_size" delta="10000" />
+         </test>
+    </tests>
+<help><![CDATA[
+
+@TIP_AND_WARNING@
+
+**Tool Description**
+
+This tool generates a hierarchical cluster heatmap from a wide format dataset.
+An option to add a hierarchical clustering dendrogram on the top of the heatmap figure is included along with an option to removal plot labels.
+
+**NOTE:** This script works best with log transformed data that contains no missing data.
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+- Two input datasets are required.
+
+	@WIDE@
+
+    **NOTE:** The sample IDs must match the sample IDs in the Design File
+    (below). Extra columns will automatically be ignored.
+
+
+	@METADATA@
+
+**In addition to your datasets, you need to provide:**
+
+**Unique Feature ID**
+
+    - The column name in your wide dataset that contains the unique IDs for
+      your features. In our example dataset you would input *Compound*.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+A PDF file with a hierarchical cluster heatmap of the data
+
+]]></help>
+    <expand macro="citations"/>
+</tool>