--- a/searchgui.xml	Tue May 15 14:50:35 2018 -0400
+++ b/searchgui.xml	Fri Jun 08 15:58:53 2018 -0400
@@ -8,14 +8,13 @@
     <requirements>
 	<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
 	<requirement type="package" version="3.0">zip</requirement>
-  <requirement type="package">JQ</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
 <![CDATA[
         #from datetime import datetime
         #import json
-        #import os;
+        #import os
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "searchgui_stderr"
@@ -27,7 +26,7 @@
         export HOME=\$cwd;
 
         ## echo the search engines to run
-        echo "$search_engines_options.engines";
+        echo '$search_engines_options.engines';
 
         ##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;
@@ -36,54 +35,27 @@
             #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
 
-
-
-        ## Necessary for executing tests. The FASTA file has to be manually copied from the test-data folder to the working directory in order it can be found when using the PAR file.
-        cp '$__tool_directory__/test-data/searchgui_tinydb1_concatenated_target_decoy.fasta' "\$cwd/searchgui_tinydb1_concatenated_target_decoy.fasta";
-
-
-
         ## copy the input .par file to the working folder
-        cp "${input_par}" "\$cwd/SEARCHGUI_IdentificationParameters.par";
-        echo "-.par source file:";
-        echo "${input_par}";
+        cp '${input_zip}' './input_par_fasta.zip';
+        echo '-.zip source file:';
+        echo '${input_zip}';
 
-        ## (local) PAR file points to a FASTA file with .dat extension, which gives problems with many search engines. We should rename it to a .fasta file before passing it to SearchGUI
-        #set $par_target_path = "$cwd/SEARCHGUI_IdentificationParameters.par";
-        echo "-.par target file:";
-        echo $par_target_path;
-
-        ## reading from the original .par file the path of the source .dat (fasta) file  to be used
-        content_par_target_path=`cat $par_target_path`;
-        dat_path=`jq -r '.searchParameters.fastaFile.path' <<< "\$content_par_target_path"`;
-        echo "-.dat file path from target .par: ";
-        echo "\$dat_path";
 
-        ## copy original .data fasta file to a local .fasta file
-        new_fasta_file_path="\$cwd/input_database.fasta";
-        cp "\$dat_path" "\$new_fasta_file_path";
-        echo "-new .fasta file path copied from source .dat file: ";
-        echo "\$new_fasta_file_path";
+        ## Necessary for executing tests. Specific par files need to be uncompressed to be used by the tool.
+        jar xvf './input_par_fasta.zip' 'Identification_Parameters_default.par' 'searchgui_tinydb1_concatenated_target_decoy.fasta';
+        jar xvf './input_par_fasta.zip' Identification_Parameters_specific.par searchgui_tinydb1_concatenated_target_decoy.fasta;
+        if [ -f ./Identification_Parameters_default.par ];then
+            mv ./Identification_Parameters_default.par ./SEARCHGUI_IdentificationParameters.par;
+        fi;
+        if [ -f ./Identification_Parameters_specific.par ];then
+            mv './Identification_Parameters_specific.par' './SEARCHGUI_IdentificationParameters.par';
+        fi;
 
-        ## modifying the .par file!!
-        ## First we establish the new content for the path: .searchParameters.fastaFile.path
-        new_content_par_target_path=`jq '.searchParameters.fastaFile.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$content_par_target_path"`;
-        ## Secondly, for .proteinInferencePreferences.proteinSequenceDatabase.path
-        new_content_par_target_path=`jq '.proteinInferencePreferences.proteinSequenceDatabase.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$new_content_par_target_path"`;
-
-        ## we generate a new .par file filled with the new fasta path.
-        #set $new_par_target_path = "$cwd/SEARCHGUI_IdentificationParameters_new.par";
-        echo "\$new_content_par_target_path" >> $new_par_target_path;
-        echo "-new par target path: ";
-        echo $new_par_target_path;
-
-        ## As PeptideShaker waits for "SEARCHGUI_IdentificationParameters.par" name, we overwrite the original file with the "_new" file
-        ##mv "\$cwd/SEARCHGUI_IdentificationParameters_new.par" "\$cwd/SEARCHGUI_IdentificationParameters.par"
-        rm $par_target_path;
-        mv $new_par_target_path $par_target_path;
+        ## By default we will always try to uncompress SEARCHGUI_IdentificationParameters.par and input_database.fasta
+        jar xvf './input_par_fasta.zip' SEARCHGUI_IdentificationParameters.par input_database.fasta;
 
 
         ################
@@ -94,7 +66,7 @@
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
-            -id_params $par_target_path
+            -id_params ./SEARCHGUI_IdentificationParameters.par
 
             -threads "\${GALAXY_SLOTS:-12}"
 
@@ -194,8 +166,8 @@
 ]]>
     </command>
     <inputs>
-        <param format="par" name="input_par" type="data" label="Identification Parameters file"
-          help="Select PAR file from history"/>
+        <param format="zip" name="input_zip" type="data" label="Identification Parameters and fasta file"
+          help="Select a zip file with Identification Parameters (.par) and a fasta file from history"/>
 
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
@@ -258,16 +230,18 @@
         <!-- Test that specifying non-default search engines works -->
         <test>
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
-            <param name="input_par" value="Identification_Parameters_specific.par"/>
+          <!--  <param name="input_par" value="Identification_Parameters_specific.par"/>-->
+            <param name="input_zip" value="IdentificationParametersAndFastaSpecific.zip" ftype="zip" />
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
-            <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>
             <param name="peak_lists" value="searchgui_smallspectra.mgf"/>
-            <param name="input_par" value="Identification_Parameters_default.par"/>
+          <!--  <param name="input_par" value="Identification_Parameters_default.par"/>-->
+            <param name="input_zip" value="IdentificationParametersAndFastaDefault.zip" ftype="zip" />
             <param name="engines" value="MS_Amanda"/>
-            <output name="output" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="searchgui_results" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
 
     </tests>