# HG changeset patch
# User rnateam
# Date 1511172243 18000
# Node ID 9ebd60531aa6ef6e8c369f07fb5edf2098691ca2
# Parent  399593f05b4d25ae7fe2d8d2e97e5eacda0908b0
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea commit 6767a5ffb02052c844e9d862c79912f998f39d8e

diff -r 399593f05b4d -r 9ebd60531aa6 mea.xml
--- a/mea.xml	Sat Aug 01 04:46:19 2015 -0400
+++ b/mea.xml	Mon Nov 20 05:04:03 2017 -0500
@@ -1,29 +1,24 @@
-<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>
     </requirements>
-    <stdio>
-        <exit_code range=":-1"/>
-        <exit_code range="1:" />
-    </stdio>
     <version_command>mea --version</version_command>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         mea
-        #if str($predict_mode.predict_selector) == "predict":
-            $predict_mode.dotplot
-            #if str($predict_mode.mea_parameters.mea_parameters_selector) == "no_default"
+        #if str($predict_mode.predict_selector) == 'predict':
+            '$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 $predict_mode.structure`
+            --structure '$predict_mode.structure'
         #end if
         #if str($compare_mode.compare_selector) == 'compare':
-            --reference `cat $compare_mode.reference`
+            --reference '$compare_mode.reference'
             $compare_mode.slide_rule
             $compare_mode.conflict_rule
         #end if
@@ -61,8 +56,16 @@
                 </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)" />
+                <param argument="--structure" type="text" label="Structure" optional="False"
+                    help="(Predicted) RNA secondary structure for comparison to a reference structure in dot-bracket format">
+                    <sanitizer>
+                        <valid>
+                            <add value="("/>
+                            <add value=")"/>
+                            <add value="."/>
+                        </valid>
+                    </sanitizer>
+                </param>
             </when>
         </conditional>
         <conditional name="compare_mode">
@@ -73,11 +76,16 @@
             </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="reference" optional="false" type="text" label="Reference"
+                       help="Reference structure in dot-bracket format">
+                   <sanitizer>
+                        <valid>
+                            <add value="("/>
+                            <add value=")"/>
+                            <add value="."/>
+                        </valid>
+                    </sanitizer>
+                </param> 
                 <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"
@@ -94,15 +102,15 @@
             <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" />
+            <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" />
             <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" />
+            <param name="structure" value=".....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))..." />
+            <param name="reference" value=".....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))" />
             <output name="stdout" file="test_compare.out" />
         </test>
     </tests>
diff -r 399593f05b4d -r 9ebd60531aa6 test-data/test_reference.txt
--- a/test-data/test_reference.txt	Sat Aug 01 04:46:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-.....(((.((((((..((......))....)))))).)))...((((((((.(((..(((....))).............))).))).)))))
diff -r 399593f05b4d -r 9ebd60531aa6 test-data/test_structure.txt
--- a/test-data/test_structure.txt	Sat Aug 01 04:46:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-.....(((.((((((..((......))....)))))).)))......(((((.(((.....(((....))).........).)).))).))...
-
diff -r 399593f05b4d -r 9ebd60531aa6 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Aug 01 04:46:19 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="gengetopt" version="2.22.6">
-        <repository changeset_revision="6071205c5cd3" name="package_gengetopt_2_22_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <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="6071205c5cd3" name="package_gengetopt_2_22_6" owner="iuc" toolshed="https://toolshed.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>
-    </package>
-</tool_dependency>