# HG changeset patch
# User rnateam
# Date 1449768128 18000
# Node ID e0f8bc01b84b1ccdb8e7d973bf13d7f469d79813
# Parent  5f780b6d99d30389c518f6eae16d53fe450ed370
planemo upload commit 9099c0a9ff5f7f3d9407e2ec3598957e02850d88-dirty

diff -r 5f780b6d99d3 -r e0f8bc01b84b mea.xml
--- a/mea.xml	Sat Aug 01 04:44:27 2015 -0400
+++ b/mea.xml	Thu Dec 10 12:22:08 2015 -0500
@@ -1,117 +1,155 @@
-<tool id="mea" name="MEA" version="0.6.4.0">
+<tool id="mea" name="MEA" version="0.6.4.1">
     <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>
+	<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:" />
+	<exit_code range=":-1"/>
+	<exit_code range="1:" />
     </stdio>
+
     <version_command>mea --version</version_command>
+
     <command><![CDATA[
         mea
-        #if str($predict_mode.predict_selector) == "predict":
+        #if str($predict_mode.predict_selector) == "predict"
             $predict_mode.dotplot
-            #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
+        	#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
+        	    --beta $predict_mode.mea_parameters.beta
+        	    --gamma $predict_mode.mea_parameters.gamma
+        	    --delta $predict_mode.mea_parameters.delta
+        	#end if
         #else
             --structure `cat $predict_mode.structure`
         #end if
-        #if str($compare_mode.compare_selector) == 'compare':
+	#if $compare_mode.compare_selector
             --reference `cat $compare_mode.reference`
             $compare_mode.slide_rule
             $compare_mode.conflict_rule
         #end if
         > $stdout
     ]]></command>
+    
     <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="True"
-                       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 value" type="float"
-                            optional="False" value="0.012"
-                            help="Slope of base pair distance penalty. (--alpha)"/>
-                    <param name="beta" label="Beta value" type="float"
-                            optional="False" value="315"
-                            help="Turning point of base pair distance penalty. (--beta)" />
-                    <param name="gamma" label="Gamma value" type="float"
-                            optional="False" value="0.5"
-                            help="Base pair weight factor. (--gamma)" />
-                    <param name="delta" label="Delta value" type="float"
-                            optional="False" value="0.003"
-                            help="Minimum penalty factor for base pairs. (--delta)" />
-                    </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. (--structure)" />
-            </when>
-        </conditional>
-        <conditional name="compare_mode">
-            <param name="compare_selector" type="select" label="Compare to a reference structure"
-                help="Whether to compare the predicted (or specified) structure to a reference structure.">
-                <option value="dont_compare">Do not compare</option>
-                <option value="compare">Compare to reference structure</option>
-            </param>
-            <when value="dont_compare" />
-            <when value="compare">
-                <param name="reference"
-                       optional="false"
-                       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="True" falsevalue="--no-slide-rule" truevalue="" help="Use slide rule. (--no-slide-rule)" />
-                <param name="conflict_rule" label="Conflict Rule" type="boolean"
-                       optional="False" checked="True" falsevalue="--no-conflict-rule" truevalue="" help="Use onflict rule. (--no-conflict-rule)"/>
-            </when>
-        </conditional>
+	<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>
+
+	
+	<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="false"
+		       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 ${on_string}" />
+	<data format="txt" name="stdout" label="${tool.name} on ${on_string}" />
     </outputs>
+    
     <tests>
-        <test>
-            <param name="mea_parameter_selector" value="default" />
-            <param name="predict_selector" value="predict" />
-            <param name="compare_selector"  value="compare" />
-            <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="compare" />
-            <param name="structure" value="test_structure.txt" />
-            <param name="reference" value="test_reference.txt" />
-            <output name="stdout" file="test_compare.out" />
-        </test>
+	<test>
+	    <param name="mea_parameter_selector" value="default" />
+
+	    <param name="predict_selector" value="predict" />
+	    <param name="compare_selector"  value="true" />
+
+	    <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>
+    
+
     <help><![CDATA[
 =====
 MEA
 =====
 
-`MEA <http://www.bioinf.uni-leipzig.de/Software/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
+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
@@ -150,7 +188,7 @@
 
 * TN   = # true negatives
 
-* SENS = TP/(TP+FN) 'Sensitivity'http://www.bioinf.uni-leipzig.de/Software/mea/
+* SENS = TP/(TP+FN) 'Sensitivity'
 
 * PPV  = TP/(TP+FP) 'Positive Predictive Value'
 
@@ -163,14 +201,23 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 * 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
+--------
+
+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>
+	<citation type="doi">10.1007/978-3-319-02624-4_1</citation>
     </citations>
+
 </tool>
diff -r 5f780b6d99d3 -r e0f8bc01b84b tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Aug 01 04:44:27 2015 -0400
+++ b/tool_dependencies.xml	Thu Dec 10 12:22:08 2015 -0500
@@ -6,19 +6,22 @@
     <package name="mea" version="0.6.4">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">
-                    http://www.bioinf.uni-leipzig.de/Software/mea/mea-0.6.4.tar.gz
-                </action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="9d2ed370989c" name="package_gengetopt_2_22_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="gengetopt" version="2.22.6" />
-                    </repository>
-                </action>
-                <action type="autoconf" />
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="set_to" name="MEA_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                </action>
+              <action type="download_by_url">
+		http://www.bioinf.uni-leipzig.de/Software/mea/mea-0.6.4.tar.gz
+	      </action>
+
+              <action type="set_environment_for_install">
+                <repository changeset_revision="9d2ed370989c" name="package_gengetopt_2_22_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                  <package name="gengetopt" version="2.22.6" />
+                </repository>
+              </action>
+	      
+              <action type="autoconf" />
+	      
+              <action type="set_environment">
+                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+		<environment_variable action="set_to" name="MEA_ROOT_PATH">$INSTALL_DIR</environment_variable>
+              </action>
             </actions>
         </install>
         <readme>Compiling MEA requires a C++ compiler (usually g++)</readme>