# HG changeset patch
# User iracooke
# Date 1433354467 14400
# Node ID cb1666df2fb3d97066dd8e43f4049cc37ba33a5e
# Parent  a9e90cdcb97a41a787d474f586fe13450b77d971
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626

diff -r a9e90cdcb97a -r cb1666df2fb3 peptide_shaker.xml
--- a/peptide_shaker.xml	Sat May 30 05:25:00 2015 -0400
+++ b/peptide_shaker.xml	Wed Jun 03 14:01:07 2015 -0400
@@ -1,9 +1,9 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="0.39.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
     <requirements>
-        <requirement type="package" version="0.38">peptide_shaker</requirement>
+        <requirement type="package" version="0.39">peptide_shaker</requirement>
     </requirements>
     <macros>
         <import>macros.xml</import>
diff -r a9e90cdcb97a -r cb1666df2fb3 searchgui.xml
--- a/searchgui.xml	Sat May 30 05:25:00 2015 -0400
+++ b/searchgui.xml	Wed Jun 03 14:01:07 2015 -0400
@@ -1,9 +1,9 @@
-<tool id="search_gui" name="Search GUI" version="1.27.0">
+<tool id="search_gui" name="Search GUI" version="1.28.0">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
     <requirements>
-        <requirement type="package" version="1.27">searchgui</requirement>
+        <requirement type="package" version="1.28">searchgui</requirement>
     </requirements>
     <macros>
         <import>macros.xml</import>
@@ -34,7 +34,7 @@
             java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
             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;
+            ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
         #end if
 
         #####################################################
@@ -48,44 +48,200 @@
 
             -db input_database.fasta
 
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
+            #if $xtandem.xtandem_advanced == "yes"
 
-                    -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
-                    -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
-                    -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
-                    -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
-                    -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
+                -xtandem_npeaks ${xtandem.xtandem_npeaks}
+                -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
+                -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}
+                -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}
+                -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}
+                -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}
+                -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} 
+				-xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} 
+				-xtandem_stp_bias ${xtandem.xtandem_stp_bias} 
+				-xtandem_evalue ${xtandem.xtandem_evalue} 
+				-xtandem_output_proteins ${xtandem.xtandem_output_proteins} 
+				-xtandem_output_sequences ${xtandem.xtandem_output_sequences} 
+				-xtandem_output_spectra ${xtandem.xtandem_output_spectra}
+				## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}
 
-                    #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
-                        -xtandem_refine 1
-                        -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
-                        -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
-                        -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
-                        -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
-                        -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
-                    #end if
+                #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+                    -xtandem_refine 1
+                    -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}
+                    -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}
+                    -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}
+                    -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}
+                    -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
+                    -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
+                    -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
+					
                 #end if
+            #end if
 
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa_hitlist_length ${advanced.omssa.hitlist_length}
-                    -omssa_remove_prec ${advanced.omssa.remove_precursor}
-                    -omssa_scale_prec ${advanced.omssa.scale_precursor}
-                    -omssa_estimate_charge ${advanced.omssa.estimate_charge}
-                #end if
+            #if $omssa.omssa_advanced == "yes"
+                -omssa_hitlist_length ${omssa.hitlist_length}
+                -omssa_remove_prec ${omssa.remove_precursor}
+                -omssa_scale_prec ${omssa.scale_precursor}
+                -omssa_estimate_charge ${omssa.estimate_charge}
+
+                -omssa_memory ${omssa.omssa_memory}
+				-omssa_isotopes ${omssa.omssa_isotopes} 
+				-omssa_neutron ${omssa.omssa_neutron} 
+				-omssa_low_intensity "${omssa.omssa_low_intensity}" 
+				-omssa_high_intensity ${omssa.omssa_high_intensity} 
+				-omssa_intensity_incr ${omssa.omssa_intensity_incr} 
+				-omssa_single_window_wd ${omssa.omssa_single_window_wd} 
+				-omssa_double_window_wd ${omssa.omssa_double_window_wd} 
+				-omssa_single_window_pk ${omssa.omssa_single_window_pk} 
+				-omssa_double_window_pk ${omssa.omssa_double_window_pk} 
+				-omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks} 
+				-omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks} 
+				-omssa_min_peaks ${omssa.omssa_min_peaks} 
+				-omssa_methionine ${omssa.omssa_methionine} 
+				-omssa_max_ladders ${omssa.omssa_max_ladders} 
+				-omssa_max_frag_charge ${omssa.omssa_max_frag_charge} 
+				-omssa_fraction ${omssa.omssa_fraction} 
+				-omssa_plus_one ${omssa.omssa_plus_one} 
+				-omssa_charge ${omssa.omssa_charge} 
+				-omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum} 
+				-omssa_forward ${omssa.omssa_forward} 
+				-omssa_rewind ${omssa.omssa_rewind} 
+				-omssa_max_frag_series ${omssa.omssa_max_frag_series} 
+				-omssa_corr ${omssa.omssa_corr} 
+				-omssa_consecutive_p ${omssa.omssa_consecutive_p} 
+				-omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue} 
+				-omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue} 
+				-omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue} 
+				-omssa_max_evalue ${omssa.omssa_max_evalue} 
+				-omssa_hitlist_charge ${omssa.omssa_hitlist_charge} 
+				-omssa_min_pep_length ${omssa.omssa_min_pep_length} 
+				-omssa_max_pep_length ${omssa.omssa_max_pep_length} 
+				-omssa_format ${omssa.omssa_format}   
+            #end if
 
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
-                    -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
-                    -msgf_termini ${advanced.msgf.msgf_termini}
-                    -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
+            #if $msgf.msgf_advanced == "yes"
+                -msgf_decoy ${msgf.msgf_decoy}
+                -msgf_min_pep_length ${msgf.msgf_min_pep_length}
+                -msgf_max_pep_length ${msgf.msgf_max_pep_length}
+                -msgf_termini ${msgf.msgf_termini}
+                -msgf_num_ptms ${msgf.msgf_num_ptms}
+                -msgf_instrument ${msgf.msgf_instrument} 
+				-msgf_fragmentation ${msgf.msgf_fragmentation}
+				-msgf_protocol ${msgf.msgf_protocol} 
+				-msgf_num_matches ${msgf.msgf_num_matches} 
+				-msgf_additional ${msgf.msgf_additional} 
+				-msgf_isotope_low ${msgf.msgf_isotope_low} 
+				-msgf_isotope_high ${msgf.msgf_isotope_high} 
+            #end if
+			
+            #if $ms_amanda.ms_amanda_advanced == "yes"
+            	 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
+    			 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
+    			 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} 
+    			 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 
+    			 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
+            # end if
+            
+            #if $myrimatch.myrimatch_advanced == "yes"
+                -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
+                -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
+                -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
+                -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
+                -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
+                -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
+                -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
+                -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
+                -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
+                -myrimatch_termini ${myrimatch.myrimatch_termini}
+                -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
+                -myrimatch_xcorr ${myrimatch.myrimatch_xcorr}
+                -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff}
+                -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
+                -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
+                -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
+                -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}	                
+            #end if
+
+            #if $tide.tide_advanced == "yes"
+                -tide_num_ptms ${tide.tide_num_ptms}
+                -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
+                -tide_min_pep_length ${tide.tide_min_pep_length}
+                -tide_max_pep_length ${tide.tide_max_pep_length}
+                -tide_min_prec_mass ${tide.tide_min_prec_mass}
+                -tide_max_prec_mass ${tide.tide_max_prec_mass}
+                -tide_decoy_format ${tide.tide_decoy_format}
+                -tide_keep_terminals ${tide.tide_keep_terminals}
+            
+                -tide_output_folder ${tide.tide_output_folder}
+                -tide_print_peptides ${tide.tide_print_peptides}
+                -tide_verbosity ${tide.tide_verbosity}
+                -tide_monoisotopic ${tide.tide_monoisotopic}
+                -tide_clip_n_term ${tide.tide_clip_n_term}
+                -tide_digestion_type ${tide.tide_digestion_type}
+                -tide_compute_sp ${tide.tide_compute_sp}
+                -tide_max_psms ${tide.tide_max_psms}
+                -tide_compute_p ${tide.tide_compute_p}
+                -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz}
+                -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz}
+                -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks}
+                -tide_spectrum_charges ${tide.tide_spectrum_charges}
+                -tide_remove_prec ${tide.tide_remove_prec}
+                -tide_remove_prec_tol ${tide.tide_remove_prec_tol}
+                -tide_progress_indicator ${tide.tide_progress_indicator}
+                -tide_use_flanking ${tide.tide_use_flanking}
+                -tide_use_neutral_losses ${tide.tide_use_neutral_losses}
+                -tide_mz_bin_width ${tide.tide_mz_bin_width}
+                -tide_mz_bin_offset ${tide.tide_mz_bin_offset}
+                -tide_concat ${tide.tide_concat}
+                -tide_export_text ${tide.tide_export_text}
+                -tide_export_sqt ${tide.tide_export_sqt}
+                -tide_export_pepxml ${tide.tide_export_pepxml}
+                -tide_export_mzid ${tide.tide_export_mzid}
+                -tide_export_pin ${tide.tide_export_pin}
+                -tide_remove_temp ${tide.tide_remove_temp}
+            #end if
+
+
+            #if $comet.comet_advanced == "yes"
+            
+            	#if $comet.comet_spectrum.comet_spectrum_selector == "yes"
+                	-comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
+                	-comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
+                	-comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}
+                	
+                	 
+                	 #if $comet.comet_spectrum.comet_remove_prec == "1"
+                		-comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                	 #end if
+                	 
+                	 #if $comet.comet_spectrum.comet_remove_prec == "2"
+                		-comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                	 #end if
+                	 
+                	-comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
+                	-comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
                 #end if
-
-                ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                ##end if
-
-            #end if
+                
+                #if $comet.comet_search.comet_search_selector == "yes"
+                	-comet_enzyme_type ${comet.comet_search.comet_enzyme_type}
+					-comet_isotope_correction ${comet.comet_search.comet_isotope_correction}
+					-comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass}
+					-comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass}
+					-comet_num_matches ${comet.comet_search.comet_num_matches}
+					-comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge}
+					-comet_remove_meth ${comet.comet_search.comet_remove_meth}
+					-comet_batch_size ${comet.comet_search.comet_batch_size}
+					-comet_num_ptms ${comet.comet_search.comet_num_ptms}
+				#end if
+				
+                #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
+                	-comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset}
+                	-comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
+                	-comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
+               
+                #end if
+          
+            #end if                
 
         2> $temp_stderr)
         &&
@@ -100,10 +256,13 @@
             -id_params SEARCHGUI_IdentificationParameters.parameters
 
             -threads "\${GALAXY_SLOTS:-12}"
-            -correct_titles "${correct_titles}"
-            $missing_titles
-            -mgf_splitting "${mgf_splitting}"
-            -mgf_spectrum_count "${mgf_spectrum_count}"
+
+			#if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
+		        -correct_titles "${searchgui_advanced.correct_titles}"
+		        $searchgui_advanced.missing_titles
+		        -mgf_splitting "${searchgui_advanced.mgf_splitting}"
+		        -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
+			#end if
 
             ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
             ## the tree is generated afterwards in PeptideShaker
@@ -111,54 +270,55 @@
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-                    -xtandem 1
-                #else
-                    -xtandem 0
-                #end if
+			#set $engines_list = str($engines).split(',')
+			#if 'X!Tandem' in $engines_list:
+            ##if str($XTANDEM_selector) == 'True'
+                -xtandem 1
+            #else
+                -xtandem 0
+            #end if
 
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa 1
-                #else
-                    -omssa 0
-                #end if
+			#if 'MyriMatch' in $engines_list:
+            ##if str($MYRIMATCH_selector) == "True"
+                -myrimatch 1
+            #else
+                -myrimatch 0
+            #end if
 
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf 1
-                #else
-                    -msgf 0
-                #end if
+			#if 'MSGF' in $engines_list:
+            ##if str($MSGF_selector) == "True"
+                -msgf 1
+            #else
+                -msgf 0
+            #end if
 
-                #if $advanced.myrimatch.myrimatch_selector == "yes"
-                    -myrimatch 1
-                #else
-                    -myrimatch 0
-                #end if
+			#if 'OMSSA' in $engines_list:
+            ##if str($OMSSA_selector) == "True"
+                -omssa 1
+            #else
+                -omssa 0
+            #end if
 
-                #if $advanced.comet.comet_selector == "yes"
-                    -comet 1
-                #else
-                    -comet 0
-                #end if
+			#if 'Comet' in $engines_list:
+            ##if str($COMET_selector) == "True"
+                -comet 1
+            #else
+                -comet 0
+            #end if
 
-                #if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                    -ms_amanda 1
-                #else
-                    -ms_amanda 0
-                #end if
+			#if 'Tide' in $engines_list:
+            ##if str($TIDE_selector) == "True"
+                -tide 1
+            #else
+                -tide 0
+            #end if
 
-                #if $advanced.tide.tide_selector == "yes"
-                    -tide 1
-                #else
-                    -tide 0
-                #end if
+            #if 'MS_Amanda' in $engines_list:
+                -ms_amanda 1
+            #else
+                -ms_amanda 0
+            #end if
 
-            #else
-                -ms_amanda 0 -tide 0
-            #end if
-            
             ## single zip file
             -output_option 0
 
@@ -179,6 +339,7 @@
 ]]>
     </command>
     <inputs>
+
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
 
@@ -189,151 +350,537 @@
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
 
-        <expand macro="general_options"/>
-
-        <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
-            help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
-            <option value="0">no correction</option>
-            <option value="1" selected="True">rename spectra</option>
-            <option value="2">delete spectra</option>
+	    <!-- Search Engine Selection -->
+        <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
+            <option value="X!Tandem" selected="True">X!Tandem</option>
+            <option value="MyriMatch">MyriMatch</option>
+            <option value="MS_Amanda">MS_Amanda</option> 
+            <option value="MSGF" selected="True">MS-GF+</option>
+            <option value="OMSSA" selected="True">OMSSA</option>
+            <option value="Comet">Comet</option>
+            <option value="Tide">Tide</option>
+            <validator type="no_options" message="Please select at least one output file" />
         </param>
 
-        <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
-            label="Add missing spectrum titles" help="(-missing_titles)"/>
+
 
-        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
+		<!-- General Parameters -->
+        <expand macro="general_options"/>
 
-        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
-
-        <conditional name="advanced">
-            <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
-                <option value="basic" selected="True">Basic</option>
+		<!-- Optional Advanced SearchGUI Parameters -->
+        <conditional name="searchgui_advanced">
+            <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
+                <option value="basic" selected="True">Default</option>
                 <option value="advanced">Advanced</option>
             </param>
             <when value="basic" />
             <when value="advanced">
-                <conditional name="xtandem">
-                    <param name="xtandem_selector" type="select" label="Run X!Tandem search">
-                        <option value="yes" selected="True">Search with X!Tandem</option>
-                        <option value="no">No X!Tandem search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="xtandem_npeaks" type="integer" value="50" 
-                            label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
-                        <param name="xtandem_min_peaks" type="integer" value="15" 
-                            label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
-                        <param name="xtandem_min_frag_mz" type="integer" value="200" 
-                            label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                        <param name="xtandem_min_prec_mass" type="integer" value="200" 
-                            label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                        <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
-                            label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+		    <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
+		        help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
+		        <option value="0">no correction</option>
+		        <option value="1" selected="True">rename spectra</option>
+		        <option value="2">delete spectra</option>
+		    </param>
+
+		    <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
+		        label="Add missing spectrum titles" help="(-missing_titles)"/>
+
+		    <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
+		        help="Choose a smaller value if you are running on a machine with limited memory"/>
+
+		    <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
+		        help="Choose a smaller value if you are running on a machine with limited memory"/>
+        </when>
+        </conditional>
 
-                        <conditional name="xtandem_refine"><!-- -xtandem_refine -->
-                            <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
-                                <option value="no" selected="True">Don't refine</option>
-                                <option value="yes" >Use refinement</option>
-                            </param>
-                            <when value="no"/>
-                            <when value="yes">
-                                <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0"
-                                    label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
-                                <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
-                                <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
-                                <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
-                                <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
-                            </when>
-                        </conditional>
+     
+    	<!-- X!TANDEM ADVANCED PARAMETERS -->
+        <conditional name="xtandem">
+            <param name="xtandem_advanced" type="select" label="X!Tandem Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+            	<param name="xtandem_npeaks" type="integer" value="50" 
+                    label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
+                <param name="xtandem_min_peaks" type="integer" value="15" 
+                    label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
+                <param name="xtandem_min_frag_mz" type="integer" value="200" 
+                    label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
+                <param name="xtandem_min_prec_mass" type="integer" value="200" 
+                    label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+                <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
+                    label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+				<param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
+					label="X!Tandem: Dynamic Range" value="100" type="integer" />
+				<param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
+					label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+				<param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
+					label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 
+				<param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
+					label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 
+				<param name="xtandem_evalue" help="Highest value for recorded peptides"
+					label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
+				<param name="xtandem_output_proteins" help="Controls output of protein sequences"
+					label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+				<param name="xtandem_output_sequences" help="Controls output of sequence information"
+					label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+				<param name="xtandem_output_spectra" help="Controls output of spectrum information"
+					label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+				<!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
+					
+                <conditional name="xtandem_refine"><!-- -xtandem_refine -->
+                    <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+                        <option value="no" selected="True">Don't refine</option>
+                        <option value="yes" >Use refinement</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
+                        <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
+                        <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
+                        <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
+                        <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
+                        <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
+                        <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
+							label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
                     </when>
                 </conditional>
+            </when>
+        </conditional>
+						
+		<!-- OMSSA ADVANCED PARAMETERS -->
+        <conditional name="omssa">
+            <param name="omssa_advanced" type="select" label="OMSSA Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
+                <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
+                <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
+                <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                
+                <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                	label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
+    	  		<!-- param name="omssa_isotopes" type="integer" value="0" 
+    	  			label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
+   	    		<param name="omssa_neutron" type="float" value="1446.94" 
+   	    			label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
+    	    	<param name="omssa_low_intensity" type="float" value="0.0" 
+    	    		label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
+    	    	<param name="omssa_high_intensity" type="float" value="0.2" 
+    	    		label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
+   	    		<param name="omssa_intensity_incr" type="float" value="0.0005" 
+   	    			label="OMSSA: Intensity Increment" help="Intensity increment" />
+    	    	<param name="omssa_single_window_wd" type="integer" value="27" 
+    	    		label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
+    	    	<param name="omssa_double_window_wd" type="integer" value="14" 
+    	    		label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
+    	    	<param name="omssa_single_window_pk" type="integer" value="2" 
+    	    		label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
+    	    	<param name="omssa_double_window_pk" type="integer" value="2" 
+    	    		label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
+    	    	<param name="omssa_min_ann_int_pks" type="integer" value="6" 
+    	    		label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
+        		<param name="omssa_min_annotated_peaks" type="integer" value="2" 
+        			label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
+   	    		<param name="omssa_min_peaks" type="integer" value="4" 
+   	    			label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
+    	    	<param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
+    	    		label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
+    	    	<param name="omssa_max_ladders" type="integer" value="128" 
+    	    		label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
+    	    	<param name="omssa_max_frag_charge" type="integer" value="2" 
+    	    		label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
+    	    	<param name="omssa_fraction" type="float" value="0.95" 
+    	    		label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
+    	    	<param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+    	    		label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
+    	    	<param name="omssa_charge" type="select" 
+    	    		label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
+                <option value="0" >Minus</option>
+                <option value="1" selected="True">Plus</option>
+    	    	</param>
+    	    	<param name="omssa_prec_per_spectrum" type="integer" value="1" 
+    	    		label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
+    	    	<param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+    	    		label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
+    	    	<param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+    	    		label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
+				<param name="omssa_max_frag_series" type="integer" value="100" 
+    	    		label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
+    	    	<param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+    	    		label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
+    	    	<param name="omssa_consecutive_p" type="float" value="0.5" 
+    	    		label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
+    	    	<param name="omssa_it_sequence_evalue" type="float" value="0.0" 
+    	    		label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
+    	    	<param name="omssa_it_spectrum_evalue" type="float" value="0.01" 
+    	    		label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
+    	    	<param name="omssa_it_replace_evalue" type="float" value="0.01" 
+    	    		label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
+    	    	<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+    	    		label="OMSSA: Remove Precursor" help="Remove precursors" />
+				<param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"  
+    	    		label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
+    	    	<param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+    	    		label="OMSSA: Remove Precursor" help="Remove precursors" />
+    	    	<param name="omssa_max_evalue" type="float" value="100" 
+    	    		label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
+    	    	<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+    	    		label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
+    	    	<param name="omssa_it_replace_evalue" type="float" value="100" 
+    	    		label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
+    	    	<param name="omssa_hitlist_length" type="integer" value="0" 
+    	    		label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
+        		<param name="omssa_hitlist_charge" type="integer" value="30" 
+        			label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
+	   		 	<param name="omssa_min_pep_length" type="integer" value="4" 
+	   		 		label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
+	   	 		<param name="omssa_max_pep_length" type="integer" value="40" 
+	   	 			label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
+	   	 		<param name="omssa_format" label="OMSSA output format" type="select" >
+                	<option value="0" selected="True">OMX</option>
+                	<option value="1" >CSV</option>
+                </param> 
+				
+            </when>
+        </conditional>
 
-                <conditional name="omssa">
-                    <param name="omssa_selector" type="select" label="Run OMSSA search">
-                        <option value="yes" selected="True">Search with OMSSA</option>
-                        <option value="no">No OMSSA search</option>
+		<!-- MS-GF+ ADVANCED PARAMETERS -->
+        <conditional name="msgf">
+            <param name="msgf_advanced" type="select" label="MSGF Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+                <param name="msgf_min_pep_length" type="integer" value="6"
+                    label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
+                <param name="msgf_max_pep_length" type="integer" value="30" 
+                    label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
+                <param name="msgf_termini" type="select" format="text" 
+                    label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
+                    <option value="0">0 (ie non-specific cleavage)</option>
+                    <option value="1">1 (ie semi-tryptic cleavage)</option>
+                    <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
+                </param>
+                <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
+                
+			    <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
+			                	<option value="0" selected="True">Low-res LCQ/LTQ</option>
+			                	<option value="1" >High-res LTQ</option>
+			                	<option value="2" >TOF</option>
+			                	<option value="3" >Q-Exactive</option>
+			    </param>
+			    <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
+			                	<option value="0" selected="True">As written in the spectrum or CID if no info</option>
+			                	<option value="1" >CID</option>
+			                	<option value="2" >ETD</option>
+			                	<option value="3" >HCD</option>
+			    </param>
+			    <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
+			                	<option value="0" selected="True">Automatic</option>
+			                	<option value="1" >Phosphorylation</option>
+			                	<option value="2" >iTRAQ</option>
+			                	<option value="3" >iTRAQPhospho</option>
+			                	<option value="4" >TMT</option>
+			                	<option value="5" >Standard</option>
+			    </param>
+			    <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
+			    <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
+			             		<option value="0" selected="True">output basic scores only</option>
+			                	<option value="1" >output additional features</option>
+			    </param>
+			    <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
+			    <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 
+            </when>
+        </conditional>
+
+  		<!-- MS-AMANDA ADVANCED PARAMETERS  -->
+        <conditional name="ms_amanda">
+            <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
+                <option value="yes" selected="True">Advanced</option>
+                <option value="no">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+            	<param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+            		label="MS Amanda: Generate Decoys" help="generate decoys" />
+				<param name="ms_amanda_max_evalue" type="float" value="100" 
+					label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
+				<param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
+				<param name="ms_amanda_max_rank" type="integer" value="5" 
+					label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
+				<param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
+					label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
+            </when>
+        </conditional>
+		
+
+		<!-- TIDE ADVANCED PARAMETERS -->
+        <conditional name="tide">
+            <param name="tide_advanced" type="select" label="TIDE Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="tide_num_ptms" type="integer" value="100"
+                    label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
+                <param name="tide_num_ptms_per_type" type="integer" value="2"
+                    label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
+                <param name="tide_min_pep_length" type="integer" value="6"
+                    label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
+                <param name="tide_max_pep_length" type="integer" value="30"
+                    label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
+                <param name="tide_min_prec_mass" type="float" value="200.0"
+                    label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
+                <param name="tide_max_prec_mass" type="float" value="7200.0"
+                    label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
+  	<param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
+			                	<option value="none" selected="True">none</option>
+			                	<option value="shuffle" >shuffle</option>
+			                	<option value="peptide-revers" >peptide-reverse</option>
+			                	<option value="protein-reverse" >protein-reverse</option>
+	</param>
+  	<param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
+			                	<option value="N" >N</option>
+			                	<option value="C" >C</option>
+			                	<option value="NC" selected="True">NC</option>
+			                	<option value="non" >none</option>
+	</param>
+                <param name="tide_decoy_seed" type="integer" value="1"
+                    label="TIDE: Decoy Seed" help="Set the decoy seed"/>
+                <param name="tide_output_folder" type="text" value="crux-output"
+                    label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
+                <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
+  	<param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
+			                	<option value="0" >0</option>
+			                	<option value="10" >10</option>
+			                	<option value="20" >20</option>
+			                	<option value="30" selected="True">30</option>
+			                	<option value="40" >40</option>
+			                	<option value="50" >50</option>
+			                	<option value="60" >60</option>
+	</param>
+
+                <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
+                <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
+  	<param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
+			                	<option value="full-digest" selected="True">full-digest</option>
+			                	<option value="partial-digest" >partial-digest</option>
+	</param>
+                <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
+                <param name="tide_max_psms" type="integer" value="10"
+                    label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
+                <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
+                <param name="tide_min_spectrum_mz" type="float" value="0.0"
+                    label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
+                <param name="tide_max_spectrum_mz" type="float" value="100000.0"
+                    label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
+                <param name="tide_min_spectrum_peaks" type="integer" value="20"
+                    label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
+  	<param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
+			                	<option value="1" >1</option>
+			                	<option value="2" >2</option>
+			                	<option value="3" >3</option>
+			                	<option value="all" selected="True">all</option>
+	</param>
+                <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
+                <param name="tide_remove_prec_tol" type="float" value="1.5"
+                    label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
+                <param name="tide_progress_indicator" type="integer" value="1000"
+                    label="TIDE: Progress Indicator" help="Choose the progress indicator frequency  (in number of fragmentation spectra processed)"/>
+                <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
+                <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
+                <param name="tide_mz_bin_width" type="float" value="0.02"
+                    label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
+                <param name="tide_mz_bin_offset" type="float" value="0.0"
+                    label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
+                <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
+                <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
+                <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
+                <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
+                <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
+                <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
+                <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
+            </when>
+        </conditional>
+
+		<!-- MyriMatch ADVANCED PARAMETERS -->
+        <conditional name="myrimatch">
+            <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+            	<param name="myrimatch_min_pep_length"  type="integer" value="6"
+            		label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
+            	<param name="myrimatch_max_pep_length"  type="integer" value="30"
+            		label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
+            	<param name="myrimatch_min_prec_mass"  type="float" value="0.0"
+            		label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
+            	<param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
+            		label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
+            	<param name="myrimatch_isotope_low"  type="integer" value="-1"
+            		label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
+            	<param name="myrimatch_isotope_high"  type="integer" value="2"
+            		label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
+            	<param name="myrimatch_num_matches"  type="integer" value="10"
+            		label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
+            	<param name="myrimatch_num_ptms"  type="integer" value="2"
+            		label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
+			    <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
+			                	<option value="CID" selected="True">CID</option>
+			                	<option value="ETD" >ETD</option>
+			    </param>
+			    <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
+			                	<option value="0">non-tryptic</option>
+			                	<option value="1" >semi-tryptic</option>
+			                	<option value="2"  selected="True" >fully-tryptic</option>
+			    </param>					    
+            	<param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true" 
+            		label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
+            	<param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+            		label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />                		
+            	<param name="myrimatch_tic_cutoff"  type="float" value="0.98"
+            		label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />
+            	<param name="myrimatch_intensity_classes"  type="integer" value="3"
+            		label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
+            	<param name="myrimatch_class_multiplier"  type="integer" value="2"
+            		label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
+            	<param name="myrimatch_num_batches"  type="integer" value="50"
+            		label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
+            	<param name="myrimatch_max_peak"  type="integer" value="100"
+            		label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
+            </when>
+        </conditional>
+		
+		<!-- Comet ADVANCED PARAMETERS -->
+        <conditional name="comet">
+            <param name="comet_advanced" type="select" label="Comet Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+            	<!-- Spectrum Related parameters -->
+            	<conditional name="comet_spectrum">
+                    <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
+                        <option value="yes">Set Spectrum Parameters</option>
+                        <option value="no" selected="True">Keep Default Spectrum Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-                        <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                        <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-                        <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    </when>
-                </conditional>
-
-                <conditional name="msgf">
-                    <param name="msgf_selector" type="select" label="Run MSGF search">
-                        <option value="yes" selected="True">Search with MSGF</option>
-                        <option value="no">No MSGF search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="msgf_min_pep_length" type="integer" value="6"
-                            label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
-                        <param name="msgf_max_pep_length" type="integer" value="30" 
-                            label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-                        <param name="msgf_termini" type="select" format="text" 
-                            label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
-                            <option value="0">0 (ie non-specific cleavage)</option>
-                            <option value="1">1 (ie semi-tryptic cleavage)</option>
-                            <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
-                        </param>
-                        <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
-                    </when>
-                </conditional>
-
-                <conditional name="myrimatch">
-                    <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
-                        <option value="yes" selected="True">Search with MyriMatch</option>
-                        <option value="no">No MyriMatch search</option>
+                    	<param name="comet_min_peaks"  type="integer" value="10"
+                    		label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
+                    	<param name="comet_min_peak_int"  type="float" value="0.0"
+                    		label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
+                    	<param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
+					                	<option value="0"  selected="True" >off</option>
+					                	<option value="1">on</option>
+					                	<option value="2">as expected for ETD/ECD spectra</option>
+					    </param>
+					    <when value="0" />
+                    	<when value="1">
+	                    	<param name="comet_remove_prec_tol"  type="float" value="1.5"
+	                    		label="Comet: Remove Precursor Tolerance" />	
+	                    </when>
+	                    <when value="2">
+	                    	<param name="comet_remove_prec_tol"  type="float" value="1.5"
+	                    		label="Comet: Remove Precursor Tolerance" />	
+	                    </when>
+                    	<param name="comet_clear_mz_range_lower"  type="float" value="0.0"
+                    		label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
+                    	<param name="comet_clear_mz_range_upper"  type="float" value="0.0"
+                    		label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />	
+					</when>
+        		</conditional>
+              	<!-- Search Related parameters -->
+            	<conditional name="comet_search">
+                    <param name="comet_search_selector" type="select" label="Comet: Search Related">
+                        <option value="yes">Set Search Parameters</option>
+                        <option value="no" selected="True">Keep Default Search Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="comet">
-                    <param name="comet_selector" type="select" label="Run Comet search">
-                        <option value="yes"  selected="True">Search with Comet</option>
-                        <option value="no">No Comet search</option>
+                    	<param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
+					                	<option value="1">semi-specific</option>
+					                	<option value="2" selected="True">full-enzyme</option>
+					                	<option value="8">unspecific N-term</option>
+					                	<option value="9">unspecific C-term</option>
+					    </param>		                    
+					    <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
+					                	<option value="0" selected="True">off</option>
+					                	<option value="1">-1,0,+1,+2,+3</option>
+					                	<option value="2">-8,-4,0,+4,+8</option>
+					    </param>
+                    	<param name="comet_min_prec_mass"  type="float" value="0.0"
+                    		label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
+                    	<param name="comet_max_prec_mass"  type="float" value="10000.0"
+                    		label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
+                    	<param name="comet_num_matches"  type="integer" value="10"
+                    		label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
+                    	<param name="comet_max_frag_charge"  type="integer" value="3"
+                    		label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
+            			<param name="comet_remove_meth"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+            				label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
+                    	<param name="comet_batch_size"  type="integer" value="0"
+                    		label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
+                    	<param name="comet_num_ptms"  type="integer" value="10"
+                    		label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />	
+					</when>
+        		</conditional>
+        		<!-- Fragment Ions Related parameters -->
+            	<conditional name="comet_fragment_ions">
+                    <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
+                        <option value="yes">Set Fragment Ions Parameters</option>
+                        <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="ms_amanda">
-                    <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
-                        <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">
-                    </when>
-                </conditional>
-
-                <conditional name="tide">
-                    <param name="tide_selector" type="select" label="Run Tide search">
-                        <option value="yes">Search with Tide</option>
-                        <option value="no" selected="True">No Comet search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
+                    	<param name="comet_frag_bin_offset"  type="float" value="0.4"
+                    		label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
+                    	<param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    		label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
+                    	<param name="comet_theoretical_fragment_ions"  type="integer" value="0"
+                    		label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />		                    	
+					</when>
+        		</conditional>
+   			                   		
             </when>
-        </conditional>
+        </conditional>          	
     </inputs>
     <outputs>
-        <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
+        <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
@@ -344,21 +891,26 @@
             <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="xtandem_selector.xtandem_refine_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="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> 
+            <param name="XTANDEM_selector" value="True"/>
+            <param name="xtandem.xtandem_advanced" value="yes"/>
+            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
+            <param name="OMSSA_selector" value="False"/>
+            <param name="MSGF_selector" value="True"/>
+            <param name="TIDE_selector" value="False"/>
+            <param name="MYRIMATCH_selector" value="False"/>
+            <param name="COMET_selector" value="False"/>
+            <param name="MS_AMANDA_selector" value="False"/>
+
+            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 
         </test>
     </tests>
     <help>
 **What it does**
 
 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
+Default: 	X! Tandem, OMSSA and MS-GF+ are executed.
+Optional: 	MyriMatch, MS-Amanda, Comet and Tide can be executed.
 
-By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run.
 
     </help>
     <expand macro="citations" />
diff -r a9e90cdcb97a -r cb1666df2fb3 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 30 05:25:00 2015 -0400
+++ b/tool_dependencies.xml	Wed Jun 03 14:01:07 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="searchgui" version="1.27">
-        <repository changeset_revision="6f6961d6bea5" name="package_searchgui_1_27" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="1.28">
+        <repository changeset_revision="ec9887977acc" name="package_searchgui_1_28" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.38">
-        <repository changeset_revision="3b8f4f9f93d2" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="0.39">
+        <repository changeset_revision="dd1e1469833f" name="package_peptideshaker_0_39" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>