--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmFinder.xml	Fri Dec 16 07:34:34 2016 -0500
@@ -0,0 +1,69 @@
+<tool id="cmFinder" name="CMFinder_v0" version="0.1.0" >
+	<requirements>
+		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
+		<requirement type="package" version='0.2'>cmfinder</requirement>
+		<requirement type="package" version='2.2.10'>viennarna</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+	<command>
+		<![CDATA[
+
+        python '$__tool_directory__/cmFinder.py' '$model_tree_stk' '$cmfinder_fa' ''
+        $gap_threshold_opts.gap_threshold_opts_selector
+        #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
+          $gap_threshold_opts.gap
+        #end if
+
+]]>
+	</command>
+	<inputs>
+		<param name="model_tree_stk" type="data"  format="stockholm" label="model_tree_stk" help="" />
+		<param name="cmfinder_fa" type="data"  format="text" label="cmfinder_fa" help="" />
+		<conditional name="gap_threshold_opts">
+			<param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
+				<option value="--g" selected="true">Yes (--g)</option>
+				<option value="">No</option>
+			</param>
+			<when value="--g">
+				<param name="gap" type="float" value="1.0" size="5"
+                        label="Define the gap threshold to determine the conserved column (--g)" help=""/>
+			</when>
+			<when value=""/>
+		</conditional>
+	</inputs>
+	<outputs>
+		<data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="model_tree_stk" value="in.model.tree.stk"/>
+			<param name="cmfinder_fa" value="cmfinder.fa"/>
+			<param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
+			<param name="gap_threshold_opts.gap" value="1.0"/>
+			<output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
+		</test>
+	</tests>
+	<help>
+		<![CDATA[
+**What it does**
+
+At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
+motives for sequences.
+]]>
+	</help>
+	<citations>
+    <citation type="bibtex">@inproceedings{costa2010fast,
+        title={Fast neighborhood subgraph pairwise distance kernel},
+        author={Costa, Fabrizio and De Grave, Kurt},
+        booktitle={Proceedings of the 26th International Conference on Machine Learning},
+        pages={255--262},
+        year={2010},
+        organization={Omnipress}
+      }
+      </citation>
+      <citation type="doi">10.1093/bioinformatics/btk008</citation>
+      <citation type="doi">10.1186/1748-7188-6-26</citation>
+  </citations>
+</tool>