--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Marea/marea_cluster.xml	Tue Nov 06 03:16:21 2018 -0500
@@ -0,0 +1,97 @@
+<tool id="MaREA_cluester" name="MaREA cluster analysis">
+    <description>of Reaction Activity Scores</description>
+    <requirements>
+        <requirement type="package">pandas</requirement>
+        <requirement type="package">scikit-learn</requirement>
+        <requirement type="package">scipy</requirement>
+        <requirement type="package">matplotlib</requirement>
+        <requirement type="package">cobrapy</requirement>
+        <requirement type="package">python-libsbml</requirement>
+    </requirements>
+    <command>
+        <![CDATA[
+      	python $__tool_directory__/marea_cluster.py
+        --rules_selector $cond_rule.rules_selector
+        #if $cond_rule.rules_selector == 'Custom':
+            --custom ${cond_rule.Custom_rules}
+        #end if
+        --cond_hier $cond_hier.hier
+        #if $cond_hier.hier == 'yes':
+            --linkage ${cond_hier.linkage}
+            --dendro $dendrogram
+        #end if
+        --k_max $k_max
+        --k_min $k_min
+        --data $input
+        --name $name
+      	--none $None
+      	--tool_dir $__tool_directory__
+        --out_log $log
+        --elbow $elbow
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="cond_rule">
+            <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:">
+                <option value="HMRcore" selected="true">HMRcore rules</option>
+                <option value="Recon">Recon 2.2 rules</option>
+                <option value="Custom">Custom rules</option>
+            </param>
+            <when value="Custom">
+                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/>
+            </when>
+        </conditional>
+        <param name="input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/>
+        <param name="name" type="text" label="Output name prefix" value = "dataset"/>
+        <param name="k_min" type="integer" size="20" value="3" min="2" max="30" label="min number of clusters (k) to be tested (k-means)"/>
+        <param name="k_max" type="integer" size="20" value="3" min="2" max="30" label="max number of clusters (k) to be tested (k-means)"/>
+        <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="if NO is selected (A and NaN) is solved as (NaN)"/>
+	<conditional name="cond_hier">
+            <param name="hier" type="select" label="Produce dendrogram (hierarchical clustering):">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="yes">
+                <param name="linkage" type="select" label="Linkage type:">
+                    <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
+                    <option value="complete">Complete: maximum distance between all observations of two sets</option>
+                    <option value="average">Average: average distance between all observations of two sets</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="txt" name="log" label="Log"/>
+        <data format="pdf" name="dendrogram" label="$name dendrogram">
+            <filter>cond_hier['hier'] == 'yes'</filter>
+        </data>
+        <data format="pdf" name="elbow" label="$name elbow evaluation method"/>
+        <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
+            <discover_datasets pattern="__name_and_ext__" directory="cluster_out"/>
+        </collection>
+    </outputs>
+    <help>
+
+.. class:: warningmark
+
+This tool expects input datasets consisting of tab-delimited columns.
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation > Convert delimiters to TAB*
+
+    </help>
+</tool>
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