diff tools/correlation_clustering/correlation_clustering.xml @ 0:6a73638d707c draft

Initial Upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/correlation_clustering/correlation_clustering.xml	Fri Nov 16 15:28:27 2018 -0500
@@ -0,0 +1,31 @@
+<tool id="correlation_clustering" name="PathOGiST - Correlation Clustering" version="1.0.0">
+    <description>: Runs correlation clustering on a distance matrix file</description>
+    <requirements>
+        <requirement type="package" version="0.0.1">pathogist</requirement>
+    </requirements>
+
+    <command><![CDATA[
+        PATHOGIST correlation $constraints $distance $threshold cc.tsv
+    ]]></command>
+
+    <inputs>
+        <param name="distance" type="data" format="tabular,txt" label="Distance Matrix"/>
+        <param name="threshold" type="integer" value="0" label="Threshold Value"
+               help="The threshold value can be determined by visualizing the distance matrix"/>
+        <param name="constraints" type="boolean" checked="false" truevalue="--all_constraints" falsevalue=""
+               label="All Constraints"
+               help="Add all constraints to the optimization problem, not just those with mixed signs"/>
+    </inputs>
+
+    <outputs>
+        <data name="clustering" label="Correlation clustering of ${on_string}" format="tabular" from_work_dir="cc.tsv"/>
+    </outputs>
+
+    <help>
+
+    </help>
+
+    <citations>
+
+    </citations>
+</tool>