--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mea.xml	Wed Jul 01 09:56:14 2015 -0400
@@ -0,0 +1,189 @@
+<tool id="mea" name="MEA" version="0.6.4">
+  <description>Predict maximum expected accuracy secondary structures
+  of RNAs and compare RNA secondary structures</description>
+  
+  <requirements>
+    
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  
+  <command><![CDATA[
+  mea
+  #if str($mode.mode_selector) == "predict"
+    $mode.dotplot
+  #else
+    --structure `cat $mode.structure`
+  #end if
+  #if str($reference) != ""
+    --reference `cat $reference`
+  #end if
+  --alpha $mode.alpha
+  --beta $mode.beta
+  --gamma $mode.gamma
+  --delta $mode.delta
+  $slide_rule
+  $conflict_rule
+  > $stdout
+  ]]></command>
+  
+  <inputs>
+    <conditional name="mode">
+      <param name="mode_selector" type="select" label="Working Mode">
+	<option value="predict">Predict</option>
+	<option value="compare">Compare</option>
+      </param>
+      <when value="predict">
+	<param name="dotplot" type="data" format="rna_eps" label="Dotplot"
+	       optional="false" help="Dotplot file (RNA base pair probabilities)"/>
+	<param name="alpha" label="Alpha" type="float"
+	   optional="false" value="0.012"
+	   help="Slope of base pair distance penalty"/>
+	<param name="beta" label="Beta" type="float"
+	       optional="false" value="315"
+	       help="Turning point of base pair distance penalty" />
+	<param name="gamma" label="Gamma" type="float"
+	       optional="false" value="0.5"
+	       help="Base pair weight factor" />
+	<param name="delta" label="Delta" type="float"
+	       optional="false" value="0.003"
+	       help="Minimum penalty factor for base pairs" />
+      </when>
+      <when value="compare">
+	<param name="structure" format="txt" type="data" label="Structure"
+	       optional="false" help="(Predicted) RNA secondary structure" />
+      </when>
+    </conditional>
+    
+    <param name="reference" format="txt" type="data" label="Reference" />
+
+    <param name="slide_rule" label="Slide Rule" type="boolean"
+	   optional="false"
+ 	   checked="yes"
+	   falsevalue="--no-slide-rule" truevalue=""
+	   help="Use slide rule" />
+    <param name="conflict_rule" label="Conflict Rule" type="boolean"
+	   optional="false"
+	   checked="yes"
+	   falsevalue="--no-conflict-rule" truevalue=""
+	   help="Use onflict rule"/>
+  </inputs>
+  
+  <outputs>
+    <data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="alpha"
+	     value="0.012" />
+      <param name="beta" 
+	     value="315" />
+      <param name="gamma"
+	     value="0.5" />
+      <param name="delta"
+	     value="0.003" />
+      <param name="slide-rule" checked="yes" />
+      <param name="conflict-rule" checked="yes" />
+
+      <param name="mode_selector" value="predict" />
+      <param name="reference" value="test_reference.txt" />
+      
+      <param name="dotplot" value="test_dp.ps" />
+
+      <output name="stdout" file="test_predict.out" />
+    </test>
+    
+    <test>
+      <param name="mode_selector" value="compare" />
+      <param name="structure" value="test_structure.txt" />
+      <param name="reference" value="test_reference.txt" />
+      <param name="slide-rule" checked="yes" />
+      <param name="conflict-rule" checked="yes" />
+
+      <output name="stdout" file="test_compare.out" />
+    </test>
+  </tests>
+  
+
+  <help><![CDATA[
+===
+MEA
+===
+  
+MEA predicts RNA maximum expected accuracy structures from RNA base
+pair probabilities and optionally compares them to a reference
+structure. In a special mode it skips the prediction and compares a
+given structure to the reference.  For the prediction, MEA allows to
+penalize long base pairs, using parameters alpha, beta, gamma, and
+delta. For the comparison of secondary structures, several measures
+are computed from the confusion matrix of the RNA base pairs.
+
+------
+Inputs
+------
+  
+The tool accepts dot plot files as generated by RNAfold -p.
+
+For (predicted) structure and reference, the tool accepts
+dot-bracket structures with pseudoknots (supporting bracket pairs
+(),{},[],<>,Aa,Bb,...)
+
+-------
+Outputs
+-------
+  
+If predicting a structure, the tool outputs the sequence and the
+predicted dot bracket strucuture with computed score in parenthesis
+following the structure. This mimicks the output of the Vienna
+tools.
+  
+The result of structure comparison is reported as a line of numbers
+  
+  TP FP FN TN SENS PPV F1 MCC
+  
+where 
+
+  * TP   = # true positives
+
+  * FP   = # false positives
+
+  * FN   = # false negatives
+
+  * TN   = # true negatives
+
+  * SENS = TP/(TP+FN) 'Sensitivity'
+
+  * PPV  = TP/(TP+FP) 'Positive Predictive Value'
+
+  * F1   = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise   'F1-score'
+
+  * MCC  = (TP*TN - FP*FN) / sqrt( (TP+FP)*(TP+FN)*(TN+FP)*(TN+FN) ) 'Mathews correlation coefficient'
+
+  
+Special rules for prediction evaluation:
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+  
+* Slide rule: tolerate shift of one base pair end by one base. This
+  rule directly affects the number of true positives.  
+
+* Conflict rule: predicted base pairs are false only if they
+  conflict with the reference; two base pair conflict if and only if
+  they share one end This rule directly affects the number of false
+  positives.
+
+--------
+Download
+--------
+
+The command line tool MEA is free software available for download and
+local installation at
+.. __: http://www.bioinf.uni-leipzig.de/Software/mea/
+
+]]></help>
+  <citations>
+    <citation type="doi">10.1007/978-3-319-02624-4_1</citation>
+  </citations>
+
+</tool>