# HG changeset patch
# User galaxyp
# Date 1520262574 18000
# Node ID 7963340ab569bcb0da4025ede6193df3d89b54f7
# Parent  9e20c34298e39461cb12dd5bfa5edd5263345950
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad

diff -r 9e20c34298e3 -r 7963340ab569 macros.xml
--- a/macros.xml	Tue Jan 23 08:48:07 2018 -0500
+++ b/macros.xml	Mon Mar 05 10:09:34 2018 -0500
@@ -2,7 +2,7 @@
     <xml name="stdio">
         <stdio>
             <exit_code range="1:" level="fatal" description="Job Failed" />
-            <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
+            <regex match="java.*Exception" level="fatal" description="Java Exception"/>
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
             <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
@@ -17,8 +17,8 @@
             -max_charge $precursor_options.max_charge
             -fi $precursor_options.forward_ion
             -ri $precursor_options.reverse_ion
-            -min_isotope ${precursor_options.min_isotope} 
-            -max_isotope ${precursor_options.max_isotope} 
+            -min_isotope ${precursor_options.min_isotope}
+            -max_isotope ${precursor_options.max_isotope}
             #if $protein_digest_options.digestion.cleavage == 'default':
               ## -enzyme "Trysin"
               -mc $protein_digest_options.digestion.missed_cleavages
@@ -30,7 +30,7 @@
                   #silent $enzymes.append(str($digest.enzyme))
                   #silent $missed_cleavages.append(str($digest.missed_cleavages))
                   ## #silent $specificities.append(str($digest.specificity))
-              #end for    
+              #end for
               -enzyme "#echo ','.join($enzymes)#"
               -mc "#echo ','.join($missed_cleavages)#"
               ## -specificity "#echo ','.join($specificities)#"
@@ -41,7 +41,7 @@
             #set $fixed_mods_str = $protein_modification_options.fixed_modifications or ''
             #set $variable_mods_str = $protein_modification_options.variable_modifications or ''
             #if $fixed_mods_str
-                -fixed_mods "$fixed_mods_str" 
+                -fixed_mods "$fixed_mods_str"
             #end if
             #if $variable_mods_str
                 -variable_mods "$variable_mods_str"
@@ -79,7 +79,7 @@
                             <option value="Trypsin + CNBr">Trypsin + CNBr</option>
                             <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
                             <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-                            <option value="Whole Protein">Whole Protein</option> 
+                            <option value="Whole Protein">Whole Protein</option>
                             <option value="Asp-N">Asp-N</option>
                             <option value="Glu-C">Glu-C</option>
                             <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
@@ -129,7 +129,7 @@
             <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
                 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
                 <option value="1">Parts per million (ppm)</option>
-                <option value="0">Daltons</option>
+                <option value="0" selected="true">Daltons</option>
             </param>
             <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
                 help="Provide error value for fragment ions, based on instrument used"/>
@@ -157,7 +157,7 @@
                     <column name="value" index="0" />
                 </options>
             </param>
-            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" 
+            <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
                 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
                 <options from_file="searchgui_mods.loc">
                     <column name="name" index="0" />
diff -r 9e20c34298e3 -r 7963340ab569 searchgui.xml
--- a/searchgui.xml	Tue Jan 23 08:48:07 2018 -0500
+++ b/searchgui.xml	Mon Mar 05 10:09:34 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.2">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -75,12 +75,12 @@
                 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
                 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
                 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
-                -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl} 
-                -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro} 
-                -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias} 
-                -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue} 
-                -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins} 
-                -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences} 
+                -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
+                -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
+                -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
+                -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
+                -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
+                -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
                 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
                 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
 
@@ -93,9 +93,9 @@
                     -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
                     -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
                     -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
-                    
+
                 #end if
-            #else 
+            #else
                 -xtandem_output_spectra 1
             #end if
 
@@ -105,37 +105,37 @@
                 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
                 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
                 -omssa_memory ${advanced_options.omssa.omssa_memory}
-                -omssa_neutron ${advanced_options.omssa.omssa_neutron} 
-                -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" 
-                -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} 
-                -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} 
-                -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} 
-                -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} 
-                -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} 
-                -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} 
-                -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} 
-                -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} 
-                -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} 
-                -omssa_methionine ${advanced_options.omssa.omssa_methionine} 
-                -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} 
-                -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} 
-                -omssa_fraction ${advanced_options.omssa.omssa_fraction} 
-                -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} 
-                -omssa_charge ${advanced_options.omssa.omssa_charge} 
-                -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum} 
-                -omssa_forward ${advanced_options.omssa.omssa_forward} 
-                -omssa_rewind ${advanced_options.omssa.omssa_rewind} 
-                -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series} 
-                -omssa_corr ${advanced_options.omssa.omssa_corr} 
-                -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p} 
-                -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue} 
-                -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue} 
-                -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue} 
-                -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue} 
-                -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge} 
-                -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length} 
-                -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length} 
-                -omssa_format ${advanced_options.omssa.omssa_format}   
+                -omssa_neutron ${advanced_options.omssa.omssa_neutron}
+                -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
+                -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
+                -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
+                -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
+                -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
+                -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
+                -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
+                -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
+                -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
+                -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
+                -omssa_methionine ${advanced_options.omssa.omssa_methionine}
+                -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
+                -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
+                -omssa_fraction ${advanced_options.omssa.omssa_fraction}
+                -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
+                -omssa_charge ${advanced_options.omssa.omssa_charge}
+                -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
+                -omssa_forward ${advanced_options.omssa.omssa_forward}
+                -omssa_rewind ${advanced_options.omssa.omssa_rewind}
+                -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
+                -omssa_corr ${advanced_options.omssa.omssa_corr}
+                -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
+                -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
+                -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
+                -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
+                -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
+                -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
+                -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
+                -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
+                -omssa_format ${advanced_options.omssa.omssa_format}
             #end if
 
             #if $advanced_options.msgf.msgf_advanced == "yes"
@@ -144,23 +144,20 @@
                 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
                 -msgf_termini ${advanced_options.msgf.msgf_termini}
                 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
-                -msgf_instrument ${advanced_options.msgf.msgf_instrument} 
+                -msgf_instrument ${advanced_options.msgf.msgf_instrument}
                 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
-                -msgf_protocol ${advanced_options.msgf.msgf_protocol} 
-                -msgf_num_matches ${advanced_options.msgf.msgf_num_matches} 
-                -msgf_additional ${advanced_options.msgf.msgf_additional} 
+                -msgf_protocol ${advanced_options.msgf.msgf_protocol}
+                -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
+                -msgf_additional ${advanced_options.msgf.msgf_additional}
             #end if
-            
-            #* Not working in tests
+
             #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
                  -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
-                 -ms_amanda_max_evalue ${advanced_options.ms_amanda.ms_amanda_max_evalue}
-                 -ms_amanda_instrument ${advanced_options.ms_amanda.ms_amanda_instrument} 
-                 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank} 
+                 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
+                 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
                  -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
             #end if
-            *#
-            
+
             #* Not working in tests
             #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
                 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
@@ -177,7 +174,7 @@
                 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
                 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
                 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
-                -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}                    
+                -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
             #end if
             *#
 
@@ -202,7 +199,7 @@
                 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
             #end if
             *#
- 
+
             #* Not working in tests
             #if $advanced_options.tide.tide_advanced == "yes"
                 -tide_num_ptms ${advanced_options.tide.tide_num_ptms}
@@ -213,7 +210,7 @@
                 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
                 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
                 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
-            
+
                 -tide_output_folder ${advanced_options.tide.tide_output_folder}
                 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
                 -tide_verbosity ${advanced_options.tide.tide_verbosity}
@@ -256,11 +253,11 @@
                      #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
                         -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                      #end if
-                     
+
                      #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
                         -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                      #end if
-                     
+
                     -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
                     -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
                 #end if
@@ -279,7 +276,6 @@
 
                 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
                     -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
-                    -comet_sparse_matrix ${advanced_options.comet.comet_fragment_ions.comet_sparse_matrix}
                     -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
                 #end if
             #end if
@@ -320,7 +316,7 @@
         ################
         ## Search CLI ##
         ################
-        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 
+        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
             -temp_folder `pwd`
             -spectrum_files \$cwd
@@ -447,7 +443,7 @@
             <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
                 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
-    
+
                 <option value="MSGF" selected="True">MS-GF+</option>
                 <option value="OMSSA" selected="True">OMSSA</option>
                 <option value="Comet">Comet</option>
@@ -456,7 +452,7 @@
                 <option value="Tide">Tide</option>
                 <!-- Not working in tests
                 -->
-                <option value="MyriMatch">MyriMatch</option> 
+                <option value="MyriMatch">MyriMatch</option>
                 <option value="MS_Amanda">MS_Amanda</option>
                 <!-- Windows only
                 <option value="Andromeda">Andromeda</option>
@@ -475,7 +471,7 @@
         <!-- General Parameters -->
         <expand macro="general_options"/>
 
-        
+
         <section name="advanced_options" expanded="false" title="Andvanced Options">
             <!-- Optional Advanced SearchGUI Parameters -->
             <conditional name="searchgui_advanced">
@@ -491,18 +487,18 @@
                     <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>
-    
+
             <!-- X!TANDEM ADVANCED PARAMETERS -->
             <conditional name="xtandem">
                 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
@@ -511,13 +507,13 @@
                 </param>
                 <when value="no" />
                 <when value="yes">
-                    <param name="xtandem_npeaks" type="integer" value="50" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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"/>
@@ -526,9 +522,9 @@
                     <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" /> 
+                        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" /> 
+                        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="0.01" />
                     <param name="xtandem_output_proteins" help="Controls output of protein sequences"
@@ -538,7 +534,7 @@
                     <param name="xtandem_output_spectra" help="Controls output of spectrum information"
                         label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
                     <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" 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>
@@ -564,7 +560,7 @@
                     </conditional>
                 </when>
             </conditional>
-    
+
             <!-- OMSSA ADVANCED PARAMETERS -->
             <conditional name="omssa">
                 <param name="omssa_advanced" type="select" label="OMSSA Options">
@@ -577,83 +573,83 @@
                     <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_neutron" type="float" value="1446.94" 
+                    <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" 
+                    <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" 
+                    <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" 
+                       <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                       <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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"  
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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"  
+                    <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"  
+                    <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" 
+                    <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"  
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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" 
+                    <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>
@@ -661,7 +657,7 @@
                     </param>
                 </when>
             </conditional>
-    
+
             <!-- MS-GF+ ADVANCED PARAMETERS -->
             <conditional name="msgf">
                 <param name="msgf_advanced" type="select" label="MSGF Options">
@@ -674,16 +670,16 @@
                         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" 
+                    <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="txt" 
+                    <param name="msgf_termini" type="select" format="txt"
                         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>
@@ -711,9 +707,8 @@
                     </param>
                 </when>
             </conditional>
-    
+
               <!-- MS-AMANDA ADVANCED PARAMETERS  -->
-            <!-- Not working in tests
             <conditional name="ms_amanda">
                 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
                     <option value="yes">Advanced</option>
@@ -721,20 +716,37 @@
                 </param>
                 <when value="no" />
                 <when value="yes">
-                    <param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+                    <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" 
+                    <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
+                      help="MS Amanda instrument id option. Available ion types are listed here.">
+
+                      <option value="b, y" selected="True">b, y</option>
+                      <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
+                      <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
+                      <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
+                      <option value="a, b, y" >a, b, y</option>
+                      <option value="a, b, y, Imm" >a, b, y, Imm</option>
+                      <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
+                      <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
+                      <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
+                      <option value="b, y, INT" >b, y, INT</option>
+                      <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
+                      <option value="a, b, y, INT" >a, b, y, INT</option>
+                      <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
+                      <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
+                      <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
+                      <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
+
+                    </param>
+                    <param name="ms_amanda_max_rank" type="integer" value="10"
                         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 -->
             <!-- Not working in tests
             <conditional name="tide">
@@ -783,7 +795,7 @@
                         <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"
@@ -841,7 +853,7 @@
                 </when>
             </conditional>
             -->
-    
+
             <!-- MyriMatch ADVANCED PARAMETERS -->
             <!-- Not working in tests
             <conditional name="myrimatch">
@@ -872,10 +884,10 @@
                         <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" 
+                    <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_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"
@@ -889,7 +901,7 @@
                 </when>
             </conditional>
             -->
-    
+
             <!-- Andromeda ADVANCED PARAMETERS -->
             <!-- Windows only
             <conditional name="andromeda">
@@ -923,7 +935,7 @@
                 </when>
             </conditional>
             -->
-    
+
             <!-- Comet ADVANCED PARAMETERS -->
             <conditional name="comet">
                 <param name="comet_advanced" type="select" label="Comet Options">
@@ -963,7 +975,7 @@
                             <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" />    
+                                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 -->
@@ -993,12 +1005,12 @@
                                 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" 
+                            <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" />    
+                                label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
                         </when>
                     </conditional>
                     <!-- Fragment Ions Related parameters -->
@@ -1011,10 +1023,8 @@
                         <when value="yes">
                             <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)" />                                
+                                label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
                         </when>
                     </conditional>
                 </when>
@@ -1052,7 +1062,7 @@
                     <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
                 </when>
             </conditional>
-    
+
             <conditional name="novor">
                 <param name="novor_advanced" type="select" label="Novor Options">
                     <option value="yes">Advanced</option>
@@ -1090,7 +1100,7 @@
             <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="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
         <!-- Test that search works with MSAmanda -->
         <test>
@@ -1102,7 +1112,7 @@
             <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="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
     </tests>
     <help>