# HG changeset patch
# User galaxyp
# Date 1486435975 18000
# Node ID aa3728c18bd95c2ef0fced61b9e24f2eab603412
# Parent  ba5377754cce39af87655de65dbe3a5aa350d870
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312

diff -r ba5377754cce -r aa3728c18bd9 macros.xml
--- a/macros.xml	Wed Jan 25 15:37:31 2017 -0500
+++ b/macros.xml	Mon Feb 06 21:52:55 2017 -0500
@@ -8,109 +8,159 @@
         </stdio>
     </xml>
     <token name="@GENERAL_PARAMETERS@">
-            -frag_tol "${fragment_tol}"
+            -frag_tol "${precursor_options.fragment_tol}"
             ### -frag_ppm
-            -prec_tol "${precursor_ion_tol}"
-            -prec_ppm "${precursor_ion_tol_units}"
-            ### -digestion
-            ### multiple enzymes?
-            -enzyme "${enzyme}"
-            ### -specificity
-            ### value per enzyme
-            -mc $missed_cleavages
-            #set $fixed_mods_str = $fixed_modifications or ''
-            #set $variable_mods_str = $variable_modifications or ''
+            -prec_tol "${precursor_options.precursor_ion_tol}"
+            -prec_ppm "${precursor_options.precursor_ion_tol_units}"
+
+            -min_charge $precursor_options.min_charge
+            -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} 
+            #if $protein_digest_options.digestion.cleavage == 'default':
+              ## -enzyme "Trysin"
+              -mc $protein_digest_options.digestion.missed_cleavages
+            #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0:
+              #set $enzymes = []
+              #set $missed_cleavages = []
+              ## #set $specificities = []
+              #for $i, $digest in enumerate($protein_digest_options.digestion.digests):
+                  #silent $enzymes.append(str($digest.enzyme))
+                  #silent $missed_cleavages.append(str($digest.missed_cleavages))
+                  ## #silent $specificities.append(str($digest.specificity))
+              #end for    
+              -enzyme "#echo ','.join($enzymes)#"
+              -mc "#echo ','.join($missed_cleavages)#"
+              ## -specificity "#echo ','.join($specificities)#"
+            #else:
+               -digestion $protein_digest_options.digestion.cleavage
+            #end if
+
+            #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" 
             #end if
             #if $variable_mods_str
                 -variable_mods "$variable_mods_str"
             #end if
-            -min_charge $min_charge
-            -max_charge $max_charge
-            -fi $forward_ion
-            -ri $reverse_ion
-            -min_isotope ${min_isotope} 
-            -max_isotope ${max_isotope} 
 
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
-    <token name="@SEARCHGUI_VERSION@">3.1.4</token>
+    <token name="@SEARCHGUI_VERSION@">3.2.5</token>
     <xml name="general_options">
-        <param name="precursor_ion_tol_units" type="select" label="Precursor Ion 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="2">Daltons</option>
-        </param>
-        <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
-            help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
-        <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
-            help="Provide error value for fragment ions, based on instrument used"/>
-        <param name="enzyme" type="select" label="Enzyme"
-            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
-            <option value="Trypsin">Trypsin</option>
-            <option value="Arg-C">Arg-C</option>
-            <option value="CNBr">CNBr</option>
-            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
-            <option value="Formic Acid">Formic Acid</option>
-            <option value="Lys-C">Lys-C</option>
-            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
-            <option value="Pepsin A">Pepsin A</option>
-            <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="Asp-N">Asp-N</option>
-            <option value="Glu-C">Glu-C</option>
-            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
-            <option value="Top-Down">Top-Down</option>
-            <option value="Semi-Tryptic">Semi-Tryptic</option>
-            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
-            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
-            <option value="Asp-N (DE)">Asp-N (DE)</option>
-            <option value="Glu-C (DE)">Glu-C (DE)</option>
-            <option value="Lys-N (K)">Lys-N (K)</option>
-            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
-            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
-            <option value="Semi-Glu-C">Semi-Glu-C</option>
-            <option value="LysargiNase">LysargiNase</option>
-            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
-            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
-            <option value="Semi-Arg-C">Semi-Arg-C</option>
-            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
-            <option value="Arg-N">Arg-N</option>
-            <option value="Semi-Arg-N">Semi-Arg-N</option>
-        </param>
-        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
-            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
-        <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
-            help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
-            <options from_file="searchgui_mods.loc">
-                <column name="name" index="0" />
-                <column name="value" index="0" />
-            </options>
-        </param>
-        <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" />
-                <column name="value" index="0" />
-            </options>
-        </param>
-        <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
-        <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
-        <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
-            <option value="a">a</option>
-            <option value="b" selected="true">b</option>
-            <option value="c">c</option>
-        </param>
-        <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
-            <option value="x">x</option>
-            <option value="y" selected="true">y</option>
-            <option value="z">z</option>
-        </param>
-        <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
-        <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
+
+        <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
+            <conditional name="digestion">
+                <param name="cleavage" type="select" label="Digestion">
+                    <option value="default" selected="true">Trypsin</option>
+                    <option value="0">Select Enzymes</option>
+                    <option value="1">Unspecific Cleavage</option>
+                    <option value="2">Whole Protein</option>
+                </param>
+                <when value="default">
+                    <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
+                        help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
+                </when>
+                <when value="0">
+                    <repeat name="digests" min="1" title="Enzymes">
+                        <param name="enzyme" type="select" label="Enzyme"
+                            help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
+                            <option value="Trypsin">Trypsin</option>
+                            <option value="Arg-C">Arg-C</option>
+                            <option value="CNBr">CNBr</option>
+                            <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
+                            <option value="Formic Acid">Formic Acid</option>
+                            <option value="Lys-C">Lys-C</option>
+                            <option value="Lys-C, no P rule">Lys-C, no P rule</option>
+                            <option value="Pepsin A">Pepsin A</option>
+                            <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="Asp-N">Asp-N</option>
+                            <option value="Glu-C">Glu-C</option>
+                            <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
+                            <option value="Top-Down">Top-Down</option>
+                            <option value="Semi-Tryptic">Semi-Tryptic</option>
+                            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
+                            <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
+                            <option value="Asp-N (DE)">Asp-N (DE)</option>
+                            <option value="Glu-C (DE)">Glu-C (DE)</option>
+                            <option value="Lys-N (K)">Lys-N (K)</option>
+                            <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
+                            <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
+                            <option value="Semi-Glu-C">Semi-Glu-C</option>
+                            <option value="LysargiNase">LysargiNase</option>
+                            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
+                            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
+                            <option value="Semi-Arg-C">Semi-Arg-C</option>
+                            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
+                            <option value="Arg-N">Arg-N</option>
+                            <option value="Semi-Arg-N">Semi-Arg-N</option>
+                        </param>
+                        <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
+                            help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
+                        <!--
+                        <param name="specificity" type="select" label="Specificity">
+                            <option value="0" selected="true">Specific at both termini</option>
+                            <option value="1">Semi-Specific - one terminus</option>
+                            <option value="2">Specific at the N-terminus only</option>
+                            <option value="3">Specific at the C-terminus only</option>
+                        </param>
+                        -->
+                    </repeat>
+                </when>
+                <when value="1"/>
+                <when value="2"/>
+            </conditional>
+        </section>
+
+        <section name="precursor_options" expanded="false" title="Precursor Options">
+            <param name="precursor_ion_tol_units" type="select" label="Precursor Ion 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="2">Daltons</option>
+            </param>
+            <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
+                help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
+            <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
+                help="Provide error value for fragment ions, based on instrument used"/>
+            <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
+            <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
+            <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
+                <option value="a">a</option>
+                <option value="b" selected="true">b</option>
+                <option value="c">c</option>
+            </param>
+            <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
+                <option value="x">x</option>
+                <option value="y" selected="true">y</option>
+                <option value="z">z</option>
+            </param>
+            <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
+            <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
+        </section>
+
+        <section name="protein_modification_options" expanded="false" title="Protein Modification Options">
+            <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
+                help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
+                <options from_file="searchgui_mods.loc">
+                    <column name="name" index="0" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+            <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" />
+                    <column name="value" index="0" />
+                </options>
+            </param>
+        </section>
+
     </xml>
 
     <xml name="citations">
diff -r ba5377754cce -r aa3728c18bd9 peptide_shaker.xml
--- a/peptide_shaker.xml	Wed Jan 25 15:37:31 2017 -0500
+++ b/peptide_shaker.xml	Mon Feb 06 21:52:55 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.14.6">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.13.6">peptide-shaker</requirement>
+        <requirement type="package" version="1.14.6">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -82,7 +82,7 @@
             (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
                 --exec_dir="\$cwd/${bin_dir}"
                 -in \$cwd/peptideshaker_output.zip
-                -output_file output.mzid
+                -output_file \$cwd/output.mzid
                 #if $contact_options.contact_options_selector == "yes":
                     -contact_first_name "$contact_options.contact_first_name"
                     -contact_last_name "$contact_options.contact_last_name"
@@ -337,7 +337,7 @@
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
             <param name="outputs" value="zip,3"/>
-            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" />
+            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
             <output name="output_psm">
                 <assert_contents>
                     <has_text text="cds.comp41779_c0_seq1" />
@@ -358,7 +358,7 @@
             </output>
             <output name="output_hierarchical">
                 <assert_contents>
-                    <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" />
+                    <has_text_matching expression="1.1\tcds.comp" />
                 </assert_contents>
             </output>
             <output name="output_psm">
diff -r ba5377754cce -r aa3728c18bd9 searchgui.xml
--- a/searchgui.xml	Wed Jan 25 15:37:31 2017 -0500
+++ b/searchgui.xml	Mon Feb 06 21:52:55 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -23,7 +23,7 @@
         export HOME=\$cwd;
 
         ## echo the search engines to run
-        echo "$engines";
+        echo "$search_engines_options.engines";
         echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
 
         ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
@@ -41,7 +41,7 @@
         ###########################################
         ####       Creating decoy database     ####
         ###########################################
-        #if $create_decoy:
+        #if $protein_database_options.create_decoy:
             echo "Creating decoy database.";
             searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
             rm input_database.fasta &&
@@ -59,256 +59,256 @@
             @GENERAL_PARAMETERS@
 
             -db input_database.fasta
-            #if $use_gene_mapping:
-                $use_gene_mapping
-                $update_gene_mapping
+            #if $protein_database_options.use_gene_mapping:
+                $protein_database_options.use_gene_mapping
+                $protein_database_options.update_gene_mapping
             #end if
 
-            #if $xtandem.xtandem_advanced == "yes"
+            #if $advanced_options.xtandem.xtandem_advanced == "yes"
 
-                -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}
+                -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
+                -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
+                -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
+                -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_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
+                ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
 
-                #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+                #if $advanced_options.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}
+                    -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
+                    -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
+                    -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
+                    -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
+                    -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 
                 -xtandem_output_spectra 1
             #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_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}   
+            #if $advanced_options.omssa.omssa_advanced == "yes"
+                -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
+                -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
+                -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}   
             #end if
 
-            #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} 
+            #if $advanced_options.msgf.msgf_advanced == "yes"
+                -msgf_decoy ${advanced_options.msgf.msgf_decoy}
+                -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
+                -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_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} 
             #end if
             
             #* Not working in tests
-            #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}
+            #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_mono ${advanced_options.ms_amanda.ms_amanda_mono}
             #end if
             *#
             
             #* Not working in tests
-            #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_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}                    
+            #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
+                -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
+                -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
+                -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
+                -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
+                -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
+                -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
+                -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
+                -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
+                -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
+                -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
+                -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
+                -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}                    
             #end if
             *#
 
             #* Not working in tests
-            #if $andromeda.andromeda_advanced == "yes"
-                -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
-                -andromeda_max_comb ${andromeda.andromeda_max_comb}
-                -andromeda_top_peaks ${andromeda.andromeda_top_peaks}
-                -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window}
-                -andromeda_incl_water ${andromeda.andromeda_incl_water}
-                -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia}
-                -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses}
-                -andromeda_fragment_all ${andromeda.andromeda_fragment_all}
-                -andromeda_emp_correction ${andromeda.andromeda_emp_correction}
-                -andromeda_higher_charge ${andromeda.andromeda_higher_charge}
-                -andromeda_equal_il ${andromeda.andromeda_equal_il}
-                -andromeda_frag_method ${andromeda.andromeda_frag_method}
-                -andromeda_max_mods ${andromeda.andromeda_max_mods}
-                -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
-                -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
-                -andromeda_max_psms ${andromeda.andromeda_max_psms}
-                -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode}
+            #if $advanced_options.andromeda.andromeda_advanced == "yes"
+                -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
+                -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
+                -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
+                -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
+                -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
+                -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
+                -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
+                -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
+                -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
+                -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
+                -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
+                -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
+                -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
+                -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
+                -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
+                -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
+                -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
             #end if
             *#
  
             #* Not working in tests
-            #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}
+            #if $advanced_options.tide.tide_advanced == "yes"
+                -tide_num_ptms ${advanced_options.tide.tide_num_ptms}
+                -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
+                -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
+                -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
+                -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
+                -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 ${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}
+                -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}
+                -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
+                -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
+                -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
+                -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
+                -tide_max_psms ${advanced_options.tide.tide_max_psms}
+                -tide_compute_p ${advanced_options.tide.tide_compute_p}
+                -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
+                -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
+                -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
+                -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
+                -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
+                -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
+                -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
+                -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
+                -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
+                -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
+                -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
+                -tide_concat ${advanced_options.tide.tide_concat}
+                -tide_export_text ${advanced_options.tide.tide_export_text}
+                -tide_export_sqt ${advanced_options.tide.tide_export_sqt}
+                -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml}
+                -tide_export_mzid ${advanced_options.tide.tide_export_mzid}
+                -tide_export_pin ${advanced_options.tide.tide_export_pin}
+                -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
             #end if
             *#
 
-            #if $comet.comet_advanced == "yes"
+            #if $advanced_options.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}
+                #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
+                    -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
+                    -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
 
-                    -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}
+                    -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
 
 
-                     #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
-                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+                     #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 $comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
-                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+                     #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 ${comet.comet_spectrum.comet_clear_mz_range_lower}
-                    -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
+                    -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
 
-                #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}
+                #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
+                    -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
+                    -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
+                    -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
+                    -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
+                    -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
+                    -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
+                    -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
+                    -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
+                    -comet_num_ptms ${advanced_options.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}
+                #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
 
-            #if $directtag.directtag_advanced == "yes"
-                -directag_tic_cutoff ${directtag.directag_tic_cutoff}
-                -directag_max_peak_count ${directtag.directag_max_peak_count}
-                -directag_intensity_classes ${directtag.directag_intensity_classes}
-                -directag_adjust_precursor ${directtag.directag_adjust_precursor}
-                -directag_min_adjustment ${directtag.directag_min_adjustment}
-                -directag_max_adjustment ${directtag.directag_max_adjustment}
-                -directag_adjustment_step ${directtag.directag_adjustment_step}
-                -directag_charge_states ${directtag.directag_charge_states}
-                #if str($directtag.directag_output_suffix).strip() != '':
-                -directag_output_suffix ${directtag.directag_output_suffix}
+            #if $advanced_options.directtag.directtag_advanced == "yes"
+                -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
+                -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
+                -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
+                -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
+                -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
+                -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
+                -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
+                -directag_charge_states ${advanced_options.directtag.directag_charge_states}
+                #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
+                -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
                 #end if
-                -directag_ms_charge_state ${directtag.directag_ms_charge_state}
-                -directag_duplicate_spectra ${directtag.directag_duplicate_spectra}
-                -directag_deisotoping ${directtag.directag_deisotoping}
-                -directag_isotope_tolerance ${directtag.directag_isotope_tolerance}
-                -directag_complement_tolerance ${directtag.directag_complement_tolerance}
-                -directag_tag_length ${directtag.directag_tag_length}
-                -directag_max_var_mods ${directtag.directag_max_var_mods}
-                -directag_max_tag_count ${directtag.directag_max_tag_count}
-                -directag_intensity_weight ${directtag.directag_intensity_weight}
-                -directag_fidelity_weight ${directtag.directag_fidelity_weight}
-                -directag_complement_weight ${directtag.directag_complement_weight}
+                -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
+                -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
+                -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
+                -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
+                -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
+                -directag_tag_length ${advanced_options.directtag.directag_tag_length}
+                -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
+                -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
+                -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
+                -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
+                -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
             #end if
 
-            #if $novor.novor_advanced == "yes"
-                -novor_fragmentation ${novor.novor_fragmentation}
-                -novor_mass_analyzer ${novor.novor_mass_analyzer}
+            #if $advanced_options.novor.novor_advanced == "yes"
+                -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
+                -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
             #end if
 
         2> $temp_stderr)
@@ -326,11 +326,11 @@
 
             -threads "\${GALAXY_SLOTS:-12}"
 
-            #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}"
+            #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
+                -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
+                $advanced_options.searchgui_advanced.missing_titles
+                -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
+                -mgf_spectrum_count "${advanced_options.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
@@ -339,7 +339,7 @@
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
-            #set $engines_list = str($engines).split(',')
+            #set $engines_list = str($search_engines_options.engines).split(',')
             #if 'X!Tandem' in $engines_list:
                 -xtandem 1
             #else
@@ -425,648 +425,650 @@
 
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
-
-        <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
-            label="Create a concatenated target/decoy database before running PeptideShaker"
-            help="Selecting this option will help PeptideShaker calculate FDR values" />
-
-        <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
-            label="gene mappings will be used and saved along with the project (UniProt databases only)"
+        <section name="protein_database_options" expanded="false" title="Protein Database Options">
+            <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
+                label="Create a concatenated target/decoy database before running PeptideShaker"
+                help="Selecting this option will help PeptideShaker calculate FDR values" />
+            <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
+                label="gene mappings will be used and saved along with the project (UniProt databases only)"
+                help="This should only be enabled for UniProt databaases" />
+            <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
+                label="Update gene mappings automatically from Ensembl (UniProt databases only)"
             help="This should only be enabled for UniProt databaases" />
-        <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
-            label="Update gene mappings automatically from Ensembl (UniProt databases only)"
-            help="This should only be enabled for UniProt databaases" />
-
+        </section>
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
 
         <!-- Search Engine Selection -->
-        <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>
-            <!-- Not working in tests
-            -->
-            <option value="Tide">Tide</option>
-            <!-- Not working in tests
-            -->
-            <option value="MyriMatch">MyriMatch</option> 
-            <option value="MS_Amanda">MS_Amanda</option>
-            <!-- Windows only
-            <option value="Andromeda">Andromeda</option>
-            -->
-            <!-- New with version 3.0
-            -->
-            <!--working in tests
-            -->
-            <option value="DirecTag">DirecTag</option>
-            <option value="Novor">Novor (Select for non-commercial use only)</option>
-            <validator type="no_options" message="Please select at least one output file" />
-        </param>
+        <section name="search_engines_options" expanded="false" title="Search Engine Options">
+            <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>
+                <!-- Not working in tests
+                -->
+                <option value="Tide">Tide</option>
+                <!-- Not working in tests
+                -->
+                <option value="MyriMatch">MyriMatch</option> 
+                <option value="MS_Amanda">MS_Amanda</option>
+                <!-- Windows only
+                <option value="Andromeda">Andromeda</option>
+                -->
+                <!-- New with version 3.0
+                -->
+                <!--working in tests
+                -->
+                <option value="DirecTag">DirecTag</option>
+                <option value="Novor">Novor (Select for non-commercial use only)</option>
+                <validator type="no_options" message="Please select at least one output file" />
+            </param>
+        </section>
 
 
         <!-- General Parameters -->
         <expand macro="general_options"/>
 
-        <!-- 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">
-            <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>
-
-
-        <!-- 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="0.01" />
-                <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="true" />
-                <!-- <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_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>
+        
+        <section name="advanced_options" expanded="false" title="Andvanced Options">
+            <!-- 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">
+                <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>
+    
+            <!-- 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="0.01" />
+                    <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="true" />
+                    <!-- <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>
-                <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>
-
-        <!-- 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>
+                <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_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>
+    
+            <!-- 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>
-                <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>
+                <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>
+                </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>
+                    <option value="no" selected="True">Default</option>
                 </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>
-                <option value="no" selected="True">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 -->
-        <!-- Not working in tests
-        <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>
+                <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 -->
+            <!-- Not working in tests
+            <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>
-                <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>
+                <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 -->
+            <!-- Not working in tests
+            <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>
-                <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 -->
-        <!-- Not working in tests
-        <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_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>
-        -->
-
-        <!-- Andromeda ADVANCED PARAMETERS -->
-        <!-- Windows only
-        <conditional name="andromeda">
-            <param name="andromeda_advanced" type="select" label="Andromeda Options">
-                <option value="yes">Advanced</option>
-                <option value="no" selected="True">Default</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
-                <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
-                <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
-                <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
-                <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
-                <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
-                <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
-                <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
-                <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
-                <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
-                <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
-                <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
-                   <option value="CID" selected="true">CID</option>
-                   <option value="HCD">HCD</option>
-                   <option value="EDT">EDT</option>
+                <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_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>
+            -->
+    
+            <!-- Andromeda ADVANCED PARAMETERS -->
+            <!-- Windows only
+            <conditional name="andromeda">
+                <param name="andromeda_advanced" type="select" label="Andromeda Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
                 </param>
-                <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
-                <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
-                <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
-                <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
-                <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
-            </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>
+                <when value="no" />
+                <when value="yes">
+                    <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
+                    <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
+                    <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
+                    <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
+                    <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
+                    <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
+                    <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
+                    <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
+                    <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
+                    <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
+                    <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
+                    <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
+                       <option value="CID" selected="true">CID</option>
+                       <option value="HCD">HCD</option>
+                       <option value="EDT">EDT</option>
                     </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <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" />
-                        <conditional name="comet_prec">
-                            <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>
-                        </conditional>
-                        <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">
-                        <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 name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
+                    <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
+                    <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
+                    <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
+                    <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
+                </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>
-                        <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>
+                        <when value="no" />
+                        <when value="yes">
+                            <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" />
+                            <conditional name="comet_prec">
+                                <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>
+                            </conditional>
+                            <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>
-                        <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>
+                        <when value="no" />
+                        <when value="yes">
+                            <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">
+                            <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 name="directtag">
+                <param name="directtag_advanced" type="select" label="DirectTag Options">
+                    <option value="yes">Advanced</option>
+                    <option value="no" selected="True">Default</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
+                    <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
+                    <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
+                    <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
+                    <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
+                    <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
+                    <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
+                    <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
+                    <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
+                    <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
+                    <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
+                    <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
+                        <option value="0" selected="true">no deisotoping</option>
+                        <option value="1">precursor only</option>
+                        <option value="2">precursor and candidate</option>
                     </param>
-                    <when value="no" />
-                    <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)" />                                
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <conditional name="directtag">
-            <param name="directtag_advanced" type="select" label="DirectTag Options">
-                <option value="yes">Advanced</option>
-                <option value="no" selected="True">Default</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
-                <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
-                <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
-                <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
-                <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
-                <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
-                <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
-                <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
-                <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
-                <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
-                <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
-                <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
-                    <option value="0" selected="true">no deisotoping</option>
-                    <option value="1">precursor only</option>
-                    <option value="2">precursor and candidate</option>
+                    <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
+                    <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
+                    <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
+                    <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
+                    <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
+                    <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
+                    <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
+                    <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>
+                    <option value="no" selected="True">Default</option>
                 </param>
-                <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
-                <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
-                <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
-                <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
-                <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
-                <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
-                <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
-                <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>
-                <option value="no" selected="True">Default</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
-                    <option value="HCD" selected="True">HCD</option>
-                    <option value="CID">CID</option>
-                </param>
-                <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
-                    <option value="FT" selected="True">FT</option>
-                    <option value="Trap" >Trap</option>
-                    <option value="TOF" >TOF</option>
-                </param>
-            </when>
-        </conditional>
-
+                <when value="no" />
+                <when value="yes">
+                    <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
+                        <option value="HCD" selected="True">HCD</option>
+                        <option value="CID">CID</option>
+                    </param>
+                    <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
+                        <option value="FT" selected="True">FT</option>
+                        <option value="Trap" >Trap</option>
+                        <option value="TOF" >TOF</option>
+                    </param>
+                </when>
+            </conditional>
+        </section>
     </inputs>
     <outputs>
         <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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