# HG changeset patch
# User rnateam
# Date 1424113022 18000
# Node ID 2541c3e74dfad53dd272d8b9401f4b938d2de700
# Parent  6d37d9c1e9bbe6b32acbac31c847a8fe311daa4c
Uploaded

diff -r 6d37d9c1e9bb -r 2541c3e74dfa RNAShapes.xml
--- a/RNAShapes.xml	Fri Feb 13 05:34:43 2015 -0500
+++ b/RNAShapes.xml	Mon Feb 16 13:57:02 2015 -0500
@@ -42,16 +42,24 @@
       <param name="param_num_samples" type="integer" value="1000" min="0" label="Number of Samples" help="(--numSamples) Sets the number of samples that are drawn to estimate shape probabilities."/>
     </macro>
     <macro name="macro_param_absolute_deviation">
-      <param name="param_absolute_deviation" type="float" optional="True" label="Absolute Deviation" help="(--absoluteDeviation) This sets the energy range as an absolute value of the minimum free energy. Cannot be combined with --relativeDeviation."/>
+      <param name="param_absolute_deviation" type="float" optional="True" label="Absolute Deviation" help="(--absoluteDeviation) This sets the energy range as an absolute value of the minimum free energy. Cannot be combined with --relativeDeviation.">
+        <validator type="in_range" min="0"/> 
+      </param>
     </macro>
     <macro name="macro_param_relative_deviation">
-      <param name="param_relative_deviation" type="float" optional="True" label="Relative Deviation" help="(--relativeDeviation) This sets the energy range as percentage of the minimum free energy. Cannot be combined with --absoluteDeviation."/>
+      <param name="param_relative_deviation" type="float" optional="True" label="Relative Deviation" help="(--relativeDeviation) This sets the energy range as percentage of the minimum free energy. Cannot be combined with --absoluteDeviation.">
+        <validator type="in_range" min="0"/> 
+      </param>
     </macro>
     <macro name="macro_param_window_size">
-      <param name="param_window_size" type="integer" min="1" optional="True" label="Window Size" help="(--windowSize) Activates window mode and computes substrings of this size. See below for details."/>   
+      <param name="param_window_size" type="integer" optional="True" label="Window Size" help="(--windowSize) Activates window mode and computes substrings of this size. See below for details.">   
+        <validator type="in_range" min="1"/> 
+      </param>
     </macro>
     <macro name="macro_param_window_increment">
-      <param name="param_window_increment" type="integer" min="1" optional="True" label="Window Increment" help="(--windowIncrement) Increment Size. See below for details."/>   
+      <param name="param_window_increment" type="integer" optional="True" label="Window Increment" help="(--windowIncrement) Increment Size. See below for details.">   
+        <validator type="in_range" min="1"/> 
+      </param>
     </macro>
     <macro name="macro_param_structure_probs">
       <param name="param_structure_probs" type="boolean" truevalue="1" falsevalue="0" label="Structure Probabilities" help="(--structureProbs) In addition to free energy also the probability of structures is calculated."/>
@@ -70,12 +78,11 @@
   </stdio>
 
   <command>
+  <![CDATA[
   RNAshapes 
   --mode $param_cond_mode.param_mode
-  #if $param_cond_mode.param_mode == 'outside':
-    --dotplot $param_out_dotplot
-  #else:
-    &gt; $param_out
+  #if $param_cond_mode.param_mode != 'outside':
+    > $param_out
   #end if 
   #if $varExists('param_cond_mode.param_shape_level'):
     --shapeLevel $param_cond_mode.param_shape_level
@@ -116,10 +123,11 @@
   --grammar $param_grammar
   --allowLP $param_allow_lp
   $param_in
+  ]]>
   </command>
 
   <inputs>
-    <param name="param_in" type="data" format="fasta" optional="False" label="Input: fasta file" />
+    <param name="param_in" type="data" format="fasta" optional="False" label="Input: Fasta file" />
 
     <conditional name="param_cond_mode"> 
       <param name="param_mode" type="select" label="Calculation Mode" help="(--mode) For a description of the different modes see below.">
@@ -204,13 +212,22 @@
 
   </inputs>
   <outputs>
-    <data name="param_out" format="text">
-      <filter>(param_cond_mode['param_mode'] != 'outside')</filter>
+    <data name="param_out" format="txt">
+      <filter>param_cond_mode['param_mode'] != "outside"</filter>
     </data>
-    <data name="param_out_dotplot" format="ps">
-      <filter>(param_cond_mode['param_mode'] == 'outside')</filter>
-    </data>
+    <collection name="param_out_dotplot" type="list" label="rna_eps outputs">
+      <filter>param_cond_mode['param_mode'] == "outside"</filter>
+      <discover_datasets pattern="(?P&lt;designation&gt;.*)\.ps"  ext="rna_eps" visible="true"/>
+    </collection>
   </outputs>
+    <tests>
+        <test>
+            <param name="param_in" value="rnashapes_input1.fa"/>
+            <param name="param_mode" value="mfe"/>
+            <output name="param_out" file="rnashapes_result1.txt"/>
+        </test>
+    </tests>
+
   <help>
 
 **What id does**
diff -r 6d37d9c1e9bb -r 2541c3e74dfa test-data/rnashapes_input1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnashapes_input1.fa	Mon Feb 16 13:57:02 2015 -0500
@@ -0,0 +1,6 @@
+>Ovis_aries_chr25.trna231-GluCTC (36320672-36320744)  Glu (CTC) 73 bp  Sc: 35.06
+TCCTTGGCAGTCCAGCGGTTAGGGCTTCATGCTCTCCCTGTCAAAGGCCCAGGTTCAATC
+CCTGGTCAAGGAG
+>Ovis_aries_chr2.trna2838-GluCTC (38727567-38727495)  Glu (CTC) 73 bp  Sc: 37.98
+TCTCTGGTGGTCCAGTGGCTAAGACTCTGTGCTCTCAATACAGGGCACCCAGGCTCGATC
+CCTGGTCAGGGAC
diff -r 6d37d9c1e9bb -r 2541c3e74dfa test-data/rnashapes_result1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnashapes_result1.txt	Mon Feb 16 13:57:02 2015 -0500
@@ -0,0 +1,7 @@
+>Ovis_aries_chr25.trna231-GluCTC (36320672-36320744)  Glu (CTC) 73 bp  Sc: 35.06
+     1  TCCTTGGCAGTCCAGCGGTTAGGGCTTCATGCTCTCCCTGTCAAAGGCCCAGGTTCAATCCCTGGTCAAGGAG  73
+-23.80  ((((((........((((..(((((.....)))))..)))).......(((((.......))))).)))))).  [[][]]
+
+>Ovis_aries_chr2.trna2838-GluCTC (38727567-38727495)  Glu (CTC) 73 bp  Sc: 37.98
+     1  TCTCTGGTGGTCCAGTGGCTAAGACTCTGTGCTCTCAATACAGGGCACCCAGGCTCGATCCCTGGTCAGGGAC  73
+-24.70  (((((((....((((.((....((.((((((((((......)))))))..))).))...))))))))))))).  []