# HG changeset patch
# User iracooke
# Date 1434512595 14400
# Node ID 76d14dc397ed76be24df017dbd9077d2df051989
# Parent  9d12b1d3c4efb9d5e6fd256ad6c81e2f1a50d3b6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c

diff -r 9d12b1d3c4ef -r 76d14dc397ed README.rst
--- a/README.rst	Mon Jun 08 19:54:30 2015 -0400
+++ b/README.rst	Tue Jun 16 23:43:15 2015 -0400
@@ -30,16 +30,14 @@
 MSAmanda on linux
 -----------------
 
-Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required and the libmono-system-core4.0-cil has to be installed. To check your Mono version run
- 
- 	mono -V
- 
- On ubuntu Mono can be installed as follows
+Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required.  If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
+  
+On ubuntu Mono can be installed as follows
 
- 	sudo apt-get install mono-runtime
- 	sudo apt-get install libmono-system-core4.0-cil
+	sudo apt-get install mono-runtime
+	sudo apt-get install libmono-system-core4.0-cil
 
- For more help on installing Mono please see http://www.mono-project.com/download. 
+For more help on installing Mono please see http://www.mono-project.com/download. 
 
 Note
 ----
diff -r 9d12b1d3c4ef -r 76d14dc397ed searchgui.xml
--- a/searchgui.xml	Mon Jun 08 19:54:30 2015 -0400
+++ b/searchgui.xml	Tue Jun 16 23:43:15 2015 -0400
@@ -874,7 +874,7 @@
     </outputs>
     <tests>
 
-        <!-- Test that specifying non-default search engines -->
+        <!-- Test that specifying non-default search engines works -->
         <test>
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
@@ -889,6 +889,22 @@
 
             <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 
         </test>
+
+        <!-- Test that search works with MSAmanda -->
+        <test>
+            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+            <param name="precursor_ion_tol" value="100"/>
+            <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="engines" value="MS_Amanda"/>
+
+            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 
+        </test>
+
+
     </tests>
     <help>
 **What it does**
diff -r 9d12b1d3c4ef -r 76d14dc397ed test-data/tiny_searchgui_result_amandaonly.zip
Binary file test-data/tiny_searchgui_result_amandaonly.zip has changed