# HG changeset patch
# User rnateam
# Date 1436175214 14400
# Node ID 12a975bbf94c5e7bd38e141e941c3762c350b98c
# Parent  00e0ba24886ae371eb0d153e2cdcd963ed6e817a
planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty

diff -r 00e0ba24886a -r 12a975bbf94c mea.xml
--- a/mea.xml	Wed Jul 01 10:50:29 2015 -0400
+++ b/mea.xml	Mon Jul 06 05:33:34 2015 -0400
@@ -1,118 +1,152 @@
 <tool id="mea" name="MEA" version="0.6.4.1">
-  <description>Predict maximum expected accuracy secondary structures
-  of RNAs and compare RNA secondary structures</description>
-  
-  <requirements>
-    <requirement type="package" version="2.22.6" >gengetopt</requirement>
-    <requirement type="package" version="0.6.4" >mea</requirement>
-  </requirements>
-  
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-  
-  <command><![CDATA[mea
-  #if str($mode.mode_selector) == "predict"
-    $mode.dotplot
-    --alpha $mode.alpha
-    --beta $mode.beta
-    --gamma $mode.gamma
-    --delta $mode.delta
-  #else
-    --structure `cat $mode.structure`
-  #end if
-  #if $mode.compare == "compare"
-    --reference `cat $reference`
-    $slide_rule
-    $conflict_rule
-  #end if
-  > $stdout
-  ]]></command>
-  
-  <inputs>
-    <conditional name="mode">
-      <param name="mode_selector" type="select" label="Working Mode">
-	<option value="predict">Predict</option>
-	<option value="compare">Compare</option>
-      </param>
-      <when value="predict">
-	<param name="dotplot" type="data" format="rna_eps" label="Dotplot"
-	       optional="false" help="Dotplot file (RNA base pair probabilities)"/>
-	<param name="alpha" label="Alpha" type="float"
-	       optional="false" value="0.012"
-	       help="Slope of base pair distance penalty"/>
-	<param name="beta" label="Beta" type="float"
-	       optional="false" value="315"
-	       help="Turning point of base pair distance penalty" />
-	<param name="gamma" label="Gamma" type="float"
-	       optional="false" value="0.5"
-	       help="Base pair weight factor" />
-	<param name="delta" label="Delta" type="float"
-	       optional="false" value="0.003"
-	       help="Minimum penalty factor for base pairs" />
-      </when>
-      <when value="compare">
-	<param name="structure" format="txt" type="data" label="Structure"
-	       optional="false" help="(Predicted) RNA secondary structure" />
-      </when>
-    </conditional>
+    <description>Predict MEA structures and compare structures of RNAs</description>
+    
+    <requirements>
+	<requirement type="package" version="2.22.6" >gengetopt</requirement>
+	<requirement type="package" version="0.6.4" >mea</requirement>
+    </requirements>
+    
+    <stdio>
+	<exit_code range=":-1"/>
+	<exit_code range="1:" />
+    </stdio>
+
+    <version_command>mea --version</version_command>
+
+    <command><![CDATA[
+        mea
+        #if str($predict_mode.predict_selector) == "predict"
+            $predict_mode.dotplot
+        	#if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
+                --alpha $predict_mode.mea_parameters.alpha
+        	    --beta $predict_mode.mea_parameters.beta
+        	    --gamma $predict_mode.mea_parameters.gamma
+        	    --delta $predict_mode.mea_parameters.delta
+        	#end if
+        #else
+            --structure `cat $predict_mode.structure`
+        #end if
+	#if $compare_mode.compare_selector
+            --reference `cat $compare_mode.reference`
+            $compare_mode.slide_rule
+            $compare_mode.conflict_rule
+        #end if
+        > $stdout
+    ]]></command>
     
-    <param name="reference" optional="true" format="txt" type="data" label="Reference" />
+    <inputs>
+	<conditional name="predict_mode">
+	    <param name="predict_selector" type="select" label="Predict MEA structure">
+		<option value="predict">Predict MEA structure</option>
+		<option value="compare">Specify structure (for comparison)</option>
+	    </param>
+	    <when value="predict">
+		<param name="dotplot" type="data" format="rna_eps" label="Dotplot"
+		       optional="false" help="Dotplot file (RNA base pair probabilities)"/>
+		<conditional name="mea_parameters">
+		    <param name="mea_parameters_selector"
+			   type="boolean"
+			   label="Use default parameters"
+			   truevalue="default"
+			   falsevalue="no_default"
+			   checked="yes"
+			   help="The default parameters assign a base pair weight
+				 of 0.5 and penalize long base pairs."
+			   />
+		    <when value="default" />
+		    <when value="no_default">
+			<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>
+		</conditional>
+	    </when>
+	    <when value="compare">
+		<param name="structure" format="txt" type="data" label="Structure"
+		       optional="false"
+		       help="(Predicted) RNA secondary structure
+			     for comparison to a reference structure." />
+	    </when>
+	</conditional>
 
-    <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 ${on_string}" />
-  </outputs>
-  
-  <tests>
-    <test>
-      <param name="alpha"
-	     value="0.012" />
-      <param name="beta" 
-	     value="315" />
-      <param name="gamma"
-	     value="0.5" />
-      <param name="delta"
-	     value="0.003" />
-      <param name="slide-rule" checked="yes" />
-      <param name="conflict-rule" checked="yes" />
+	
+	<conditional name="compare_mode">
+	    <param name="compare_selector"
+		   type="boolean"
+		   label="Compare to a reference structure"
+		   optional="false"
+		   checked="false"
+		   truevalue="compare"
+		   falsevalue="dont_compare"
+		   help="Whether to compare the predicted (or specified) structure
+			 to a reference structure."
+		   />
+	    <when value="dont_compare" />
+	    <when value="compare">
+		<param name="reference"
+		       optional="true"
+		       format="txt" type="data"
+		       label="Reference"
+		       help="Reference structure in dot-bracket format"/>
+		
+		<param name="slide_rule" label="Slide Rule" type="boolean"
+		       optional="false"
+ 		       checked="yes"
+		       falsevalue="--no-slide-rule" truevalue=""
+		       help="Use slide rule" />
+		<param name="conflict_rule" label="Conflict Rule" type="boolean"
+		       optional="false"
+		       checked="yes"
+		       falsevalue="--no-conflict-rule" truevalue=""
+		       help="Use onflict rule"/>
+	    </when>
+	</conditional>
+    </inputs>
+    
+    <outputs>
+	<data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
+    </outputs>
+    
+    <tests>
+	<test>
+	    <param name="mea_parameter_selector" value="default" />
 
-      <param name="mode_selector" value="predict" />
-      <param name="reference" value="test_reference.txt" />
-      
-      <param name="dotplot" value="test_dp.ps" />
+	    <param name="predict_selector" value="predict" />
+	    <param name="compare_selector"  value="true" />
 
-      <output name="stdout" file="test_predict.out" />
-    </test>
+	    <param name="dotplot" value="test_dp.ps" />
+	    <param name="reference" value="test_reference.txt" />
+	    
+	    <output name="stdout" file="test_predict.out" />
+	</test>
+	
+	<test>
+	    <param name="mea_parameter_selector" value="default" />
+	    <param name="predict_selector" value="compare" />
+	    <param name="compare_selector" value="true" />
+
+	    <param name="structure" value="test_structure.txt" />
+	    <param name="reference" value="test_reference.txt" />
+
+	    <output name="stdout" file="test_compare.out" />
+	</test>
+    </tests>
     
-    <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
+=====
 
-  <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
@@ -124,7 +158,7 @@
 ------
 Inputs
 ------
-  
+
 The tool accepts dot plot files as generated by RNAfold -p.
 
 For (predicted) structure and reference, the tool accepts
@@ -134,45 +168,45 @@
 -------
 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
-  
+
+TP FP FN TN SENS PPV F1 MCC
+
 where 
 
-  * TP   = # true positives
+* TP   = # true positives
 
-  * FP   = # false positives
+* FP   = # false positives
 
-  * FN   = # false negatives
+* FN   = # false negatives
 
-  * TN   = # true negatives
+* TN   = # true negatives
 
-  * SENS = TP/(TP+FN) 'Sensitivity'
+* SENS = TP/(TP+FN) 'Sensitivity'
 
-  * PPV  = TP/(TP+FP) 'Positive Predictive Value'
+* PPV  = TP/(TP+FP) 'Positive Predictive Value'
 
-  * F1   = PPV*SENS / (PPV+SENS), if PPV+SENS!=0; 0, otherwise   'F1-score'
+* 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'
+* 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.  
+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.
+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
@@ -181,10 +215,9 @@
 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>
+    ]]></help>
+    <citations>
+	<citation type="doi">10.1007/978-3-319-02624-4_1</citation>
+    </citations>
 
 </tool>