# HG changeset patch
# User iracooke
# Date 1399275497 14400
# Node ID 3b058d96e8a727f7c651fb2f278bc37f39706a1d
# Parent  f62545ff7fa0016d6cd8a3098c2d9c9ed917baa7
Added functional test

diff -r f62545ff7fa0 -r 3b058d96e8a7 peptide_shaker.xml
--- a/peptide_shaker.xml	Sun May 04 03:20:54 2014 -0400
+++ b/peptide_shaker.xml	Mon May 05 03:38:17 2014 -0400
@@ -158,7 +158,7 @@
         ######################
         ## PeptideShakerCLI ##
         ######################
-        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
+        java  -Xmx${java_heapsize}m -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
             -temp_folder `pwd`
             -experiment '${exp_str}'
             -sample '${samp_str}'
@@ -300,6 +300,9 @@
         <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
             help="(-mgf_spectrum_count)"/>
 
+        <param name="java_heapsize" type="integer" value="2000" label="Java Memory Limit in mb for PeptideShaker"
+            help="Increase this value if you encounter out of memory errors"/>
+
         <conditional name="species_type">
             <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
                 help="(-species_type)">
@@ -596,8 +599,8 @@
 
                 <conditional name="ms_amanda">
                     <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
-                        <option value="yes" selected="True">Search with MSGF</option>
-                        <option value="no">No MS Amanda search</option>
+                        <option value="yes">Search with MS Amanda</option>
+                        <option value="no" selected="True">No MS Amanda search</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
@@ -684,6 +687,25 @@
             <filter>'1' in outputs</filter>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="input_database" value="tinydb.fasta"/>
+            <param name="peak_lists" value="tinyspectra.mgf"/>
+            <param name="precursor_ion_tol" value="100"/>
+            <param name="java_heapsize" value="1500"/>
+            <param name="fixed_modifications" value="carbamidomethyl c"/>
+            <param name="variable_modifications" value="oxidation of m"/>
+            <param name="min_charge" value="1"/>
+            <param name="max_charge" value="3"/>
+            <param name="advanced_type_selector" value="advanced"/>
+            <param name="xtandem_selector" value="yes"/>
+            <param name="omssa_selector" value="no"/>
+            <param name="msgf_selector" value="yes"/>
+            <param name="ms_amanda_selector" value="no"/>
+            
+            <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> 
+        </test>
+    </tests>
     <help>
 **What it does**