# HG changeset patch
# User rnateam
# Date 1423069302 18000
# Node ID b82c46050674d1c8e539e3f9b8ea892448fd31a7
# Parent  031ad325017617454272a5e12fe98aef28b16723
Uploaded

diff -r 031ad3250176 -r b82c46050674 rnacofold.xml
--- a/rnacofold.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnacofold.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -53,13 +53,13 @@
     </inputs>
     <outputs>
         <data format="txt" name="tabularFile"/>
-        <data format="txt" name="structure">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" visible="true"/>
-        </data>
-        <data format="txt" name="dotplot">
+        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
+        </collection>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
             <filter>pf is True</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
-        </data>
+        </collection>
     </outputs>
     <tests>
     </tests>
diff -r 031ad3250176 -r b82c46050674 rnafold.xml
--- a/rnafold.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnafold.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -68,13 +68,14 @@
     </inputs>
     <outputs>
         <data format="tabular" name="tabular_file"/>
-        <data format="txt" name="structure">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" visible="true"/>
-        </data>
-        <data format="txt" name="dotplot">
+        <collection name="sequence_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" />
+        </collection>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
             <filter>measelect['pf'] is True</filter>
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
-        </data>
+        </collection>
+          
     </outputs>
     <tests>
     </tests>
diff -r 031ad3250176 -r b82c46050674 rnalfold.xml
--- a/rnalfold.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnalfold.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -33,7 +33,7 @@
 ]]>
     </command>
     <inputs>
-        <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
+	<param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
         <param name="span" type="integer" min="0" max="5000" value="150" label="base pair span" help="Maximal distance between two paired bases. (-L)"/>
         <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
         <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
diff -r 031ad3250176 -r b82c46050674 rnapaln.xml
--- a/rnapaln.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnapaln.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -73,9 +73,9 @@
     </inputs>
     <outputs>
         <data format="txt" name="output"/>
-        <data format="txt" name="dotplot">
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
-        </data>
+        </collection>
     </outputs>
     <tests>
     </tests>
diff -r 031ad3250176 -r b82c46050674 rnapdist.xml
--- a/rnapdist.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnapdist.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -63,8 +63,9 @@
     <outputs>
         <data format="txt" name="output"/>
         <data format="txt" name="dotplot">
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
-        </data>
+        </collection>
     </outputs>
     <tests>
     </tests>
diff -r 031ad3250176 -r b82c46050674 rnapkplex.xml
--- a/rnapkplex.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnapkplex.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -49,9 +49,9 @@
     </inputs>
     <outputs>
         <data format="txt" name="output"/>
-        <data format="txt" name="dotplot">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" visible="true"/>
-        </data>
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" />
+        </collection>
     </outputs>
     <tests>
     </tests>
diff -r 031ad3250176 -r b82c46050674 rnaplex.xml
--- a/rnaplex.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnaplex.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -77,6 +77,7 @@
         <param name="scaleAccessibility" size="8" type="float" value="1.0" label="scale all opening energy by a factor" help="--scale-accessibility"/>
         <param name="constraint" type="boolean" truevalue="--constraint" falsevalue="" checked="false" label="Calculate structures subject to constraints. Constraints have to be given in the input file" help="--constraint"/>
 
+
         <conditional name="advancedOptions">
             <param name="advancedSelector" type="select" label="advanced options">
                 <option value="basic">basic Options</option>
diff -r 031ad3250176 -r b82c46050674 rnaplfold.xml
--- a/rnaplfold.xml	Tue Feb 03 04:59:51 2015 -0500
+++ b/rnaplfold.xml	Wed Feb 04 12:01:42 2015 -0500
@@ -72,9 +72,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="dotplot">
+        <collection name="matrix_outputs" type="list" label="rna_eps outputs">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
-        </data>
+        </collection>
         <data format="tar" name="outputf"/>
     </outputs>
     <tests>