--- a/peptide_shaker.xml	Mon Mar 05 10:09:34 2018 -0500
+++ b/peptide_shaker.xml	Tue Mar 20 05:09:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.4">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.17">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.16.4">peptide-shaker</requirement>
+        <requirement type="package" version="1.16.17">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -36,6 +36,20 @@
             -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
             -out \$cwd/peptideshaker_output.cpsx
             -zip \$cwd/peptideshaker_output.zip
+            #set $cleaned_list = str($outputs).split(',')
+            #if 'cps' in $cleaned_list:
+                #silent $cleaned_list.remove('cps')
+            #end if
+            #if 'mzidentML' in $cleaned_list:
+                #silent $cleaned_list.remove('mzidentML')
+            #end if
+            #if 'zip' in $cleaned_list:
+                #silent $cleaned_list.remove('zip')
+            #end if
+            #if len($cleaned_list) > 0
+              ## Only numbers are left over. These corresponds to different reports.
+              -reports #echo ','.join($cleaned_list)#
+            #end if
 
             -threads "\${GALAXY_SLOTS:-12}"
 
@@ -107,12 +121,12 @@
                     -organization_email "galaxyp@umn.edu"
                     -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
                 #end if
-            2>> $temp_stderr) 
+            2>> $temp_stderr)
             &&
         #end if
 
         ## Generate Reports if the user has selected one of the 8 additional reports
-        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 
+        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
         ## and will not be passed to the command line
         #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
 
@@ -305,7 +319,7 @@
         <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
             <filter>'mzidentML' in outputs</filter>
         </data>
-        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
+        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
             <filter>'cps' in outputs</filter>
         </data>
         <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
@@ -406,6 +420,18 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
+            <param name="processing_options_selector" value="no"/>
+            <param name="filtering_options_selector" value="no"/>
+            <param name="outputs" value="3,cps"/>
+            <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
+            <output name="output_psm">
+                <assert_contents>
+                    <has_text text="cds.comp41779_c0_seq1" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 **What it does**