--- a/searchgui.xml	Wed Jul 11 08:14:23 2018 -0400
+++ b/searchgui.xml	Sat Sep 15 08:51:12 2018 -0400
@@ -6,11 +6,11 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
-	<requirement type="package" version="3.0">zip</requirement>
+        <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+        <requirement type="package" version="3.0">zip</requirement>
     </requirements>
     <expand macro="stdio" />
-    <command>
+    <command use_shared_home="false">
 <![CDATA[
         #from datetime import datetime
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
@@ -23,28 +23,40 @@
         cwd=`pwd`;
         export HOME=\$cwd;
 
-        ## echo the search engines to run
-        echo "$search_engines_options.engines";
-        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
+        ## echo the search engines to run (single quotes important because X!Tandem)
+        echo '$search_engines_options.engines';
+        echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}';
 
         ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
-        echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
+        echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
 
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
             #set $encoded_id = $__app__.security.encode_id($mgf.id)
-            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
+            echo 'Spectrums:${mgf.display_name}(API:${encoded_id})';
         #end for
         ##ln -s "${input_database}" input_database.fasta;
         cp "${input_database}" input_database.fasta;
 
         ###########################################
+        ####       Set paths                   ####
+        ###########################################
+        echo 'Setting paths' &&
+        searchgui eu.isas.searchgui.cmd.PathSettingsCLI
+            --exec_dir="\$cwd/${bin_dir}" 
+            -temp_folder \$cwd 
+            -log \$cwd/searchgui.log  2>> $temp_stderr &&
+
+        ###########################################
         ####       Creating decoy database     ####
         ###########################################
         #if $protein_database_options.create_decoy:
-            echo "Creating decoy database.";
-            searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
+            echo 'Creating decoy database.' &&
+            searchgui eu.isas.searchgui.cmd.FastaCLI 
+                --exec_dir="\$cwd/${bin_dir}" 
+                -in input_database.fasta
+                -decoy  2>> $temp_stderr &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
             ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
@@ -53,6 +65,7 @@
         #####################################################
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
+        echo 'setting identification parameters' &&
         (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
             --exec_dir="\$cwd/${bin_dir}"
             -out SEARCHGUI_IdentificationParameters.par
@@ -323,9 +336,9 @@
         ################
         ## Search CLI ##
         ################
+        echo 'running search gui' &&
         (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
-            -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
             -id_params SEARCHGUI_IdentificationParameters.par
@@ -1097,7 +1110,7 @@
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
             <param name="xtandem.xtandem_advanced" value="yes"/>
             <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
-            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+            <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
         <!-- Test that search works with MSAmanda -->
         <test>
@@ -1107,7 +1120,7 @@
             <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="5000" />
+            <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
 
         <!-- Test that specifying non-default search engines works using modifications -->