# HG changeset patch
# User galaxyp
# Date 1484157966 18000
# Node ID ffed32e397cb34497bedd78958a1019a1aa6ad30
# Parent  2f8e9d0351a81ce19bd0c0f820018feb8e52496a
Uploaded

diff -r 2f8e9d0351a8 -r ffed32e397cb macros.xml
--- a/macros.xml	Fri Jun 10 09:57:31 2016 -0400
+++ b/macros.xml	Wed Jan 11 13:06:06 2017 -0500
@@ -4,6 +4,7 @@
             <exit_code range="1:" level="fatal" description="Job Failed" />
             <regex match="java.*Exception" level="fatal" description="Java Exception"/> 
             <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
+            <regex match="CompomicsError" level="fatal" description="Compomics Error"/>
         </stdio>
     </xml>
     <token name="@GENERAL_PARAMETERS@">
@@ -25,8 +26,8 @@
             -fi $forward_ion
             -ri $reverse_ion
     </token>
-    <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
-    <token name="@SEARCHGUI_VERSION@">2.9</token>
+    <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
+    <token name="@SEARCHGUI_VERSION@">3.1.4</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">
diff -r 2f8e9d0351a8 -r ffed32e397cb peptide_shaker.xml
--- a/peptide_shaker.xml	Fri Jun 10 09:57:31 2016 -0400
+++ b/peptide_shaker.xml	Wed Jan 11 13:06:06 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
     <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="1.11">peptide_shaker</requirement>
+        <requirement type="package" version="1.13.6">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -15,36 +15,30 @@
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "peptideshaker_stderr"
+        #set $bin_dir = "bin"
 
 
         mkdir output_reports;
         cwd=`pwd`;
 
-        cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin;
-        tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`;
-
         ln -s '$searchgui_input' searchgui_input.zip &&
+        jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
         ######################
         ## PeptideShakerCLI ##
         ######################
-        (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI
+        (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
+            --exec_dir="\$cwd/${bin_dir}"
             -temp_folder \$cwd/PeptideShakerCLI
             -experiment '$exp_str'
             -sample '$samp_str'
             -replicate 1
             -identification_files \$cwd/searchgui_input.zip
+            -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
             -out \$cwd/peptideshaker_output.cpsx
             -zip \$cwd/peptideshaker_output.zip
 
             -threads "\${GALAXY_SLOTS:-12}"
 
-            ##Optional gene annotation parameter
-            #if $species_type.species_type_selector != 'no_species_type':
-                -species_type "${species_type.species_type_selector}"
-                -species "${species_type.species}"
-                -species_update 1
-            #end if
-
             ##Optional processing parameters:
             #if $processing_options.processing_options_selector == "yes"
                 -protein_fdr "${processing_options.protein_fdr}"
@@ -85,16 +79,33 @@
 
         #if 'mzidentML' in str($outputs).split(','):
             echo "Generating mzIdentML";
-            (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI
+            (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
+                --exec_dir="\$cwd/${bin_dir}"
                 -in \$cwd/peptideshaker_output.zip
                 -output_file output.mzid
-                -contact_first_name "Proteomics"
-                -contact_last_name "Galaxy"
-                -contact_email "galaxyp@umn.edu"
-                -contact_address "galaxyp@umn.edu"
-                -organization_name "University of Minnesota"
-                -organization_email "galaxyp@umn.edu"
-                -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
+                #if $contact_options.contact_options_selector == "yes":
+                    -contact_first_name "$contact_options.contact_first_name"
+                    -contact_last_name "$contact_options.contact_last_name"
+                    -contact_email "$contact_options.contact_email"
+                    -contact_address "$contact_options.contact_address"
+                    #if str($contact_options.contact_url).strip() != '':
+                        -contact_url = "$contact_options.contact_url"
+                    #end if
+                    -organization_name "$contact_options.organization_name"
+                    -organization_email "$contact_options.organization_email"
+                    -organization_address "$contact_options.organization_address"
+                    #if str($contact_options.organization_url).strip() != '':
+                        -organization_url = "$contact_options.organization_url"
+                    #end if
+                #else:
+                    -contact_first_name "Proteomics"
+                    -contact_last_name "Galaxy"
+                    -contact_email "galaxyp@umn.edu"
+                    -contact_address "galaxyp@umn.edu"
+                    -organization_name "University of Minnesota"
+                    -organization_email "galaxyp@umn.edu"
+                    -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
+                #end if
             2>> $temp_stderr) 
             &&
         #end if
@@ -104,7 +115,8 @@
         ## and will not be passed to the command line
         #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
 
-            (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI
+            (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
+                --exec_dir="\$cwd/${bin_dir}"
                 -temp_folder \$cwd/ReportCLI
                 -in \$cwd/peptideshaker_output.zip
                 -out_reports \$cwd/output_reports
@@ -125,6 +137,7 @@
             &&
         #end if
 
+        ## # ls -l \$cwd/output_reports/* ;
 
         #if '0' in str($outputs).split(','):
             find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
@@ -138,6 +151,10 @@
             find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
             ;
         #end if
+        #if '8' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
+            ;
+        #end if
         #if '3' in str($outputs).split(','):
             find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
             ;
@@ -172,287 +189,6 @@
                 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
             </options>
         </param>
-
-        <conditional name="species_type">
-            <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
-                help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
-                <option value="Fungi">Fungi</option>
-                <option value="Plants">Plants</option>
-                <option value="Metazoa">Metazoa</option>
-                <option value="Vertebrates">Vertebrates</option>
-                <option value="Protists">Protists</option>
-                <option value="no_species_type" selected="true">No species restriction</option>
-            </param>
-            <when value="no_species_type"/>
-            <when value="Protists">
-                <param name="species" type="select" label="The species to use for the gene annotation"
-                    help="">
-                    <option value="Albugo laibachii">Albugo laibachii</option>
-                    <option value="Bigelowiella natans">Bigelowiella natans</option>
-                    <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
-                    <option value="Emiliania huxleyi">Emiliania huxleyi</option>
-                    <option value="Entamoeba histolytica">Entamoeba histolytica</option>
-                    <option value="Giardia lamblia">Giardia lamblia</option>
-                    <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
-                    <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
-                    <option value="Leishmania major">Leishmania major</option>
-                    <option value="Paramecium tetraurelia">Paramecium tetraurelia</option>
-                    <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
-                    <option value="Phytophthora infestans">Phytophthora infestans</option>
-                    <option value="Phytophthora kernoviae">Phytophthora kernoviae</option>
-                    <option value="Phytophthora lateralis">Phytophthora lateralis</option>
-                    <option value="Phytophthora parasitica">Phytophthora parasitica</option>
-                    <option value="Phytophthora ramorum">Phytophthora ramorum</option>
-                    <option value="Phytophthora sojae">Phytophthora sojae</option>
-                    <option value="Plasmodium berghei">Plasmodium berghei</option>
-                    <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
-                    <option value="Plasmodium falciparum">Plasmodium falciparum</option>
-                    <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
-                    <option value="Plasmodium vivax">Plasmodium vivax</option>
-                    <option value="Pythium aphanidermatum">Pythium aphanidermatum</option>
-                    <option value="Pythium arrhenomanes">Pythium arrhenomanes</option>
-                    <option value="Pythium irregulare">Pythium irregulare</option>
-                    <option value="Pythium iwayamai">Pythium iwayamai</option>
-                    <option value="Pythium ultimum">Pythium ultimum</option>
-                    <option value="Pythium vexans">Pythium vexans</option>
-                    <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
-                    <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
-                    <option value="Toxoplasma gondii">Toxoplasma gondii</option>
-                    <option value="Trypanosoma brucei">Trypanosoma brucei</option>
-                </param>
-            </when>
-            <when value="Plants">
-                <param name="species" type="select" label="The species to use for the gene annotation"
-                    help="">
-                    <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option>
-                    <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option>
-                    <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option>
-                    <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option>
-                    <option value="Brassica oleracea">Brassica oleracea</option>
-                    <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option>
-                    <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option>
-                    <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option>
-                    <option value="Glycine max (Soybean)">Glycine max (Soybean)</option>
-                    <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option>
-                    <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option>
-                    <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option>
-                    <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option>
-                    <option value="Oryza brachyantha">Oryza brachyantha</option>
-                    <option value="Oryza glumaepatula">Oryza glumaepatula</option>
-                    <option value="Oryza meridionalis">Oryza meridionalis</option>
-                    <option value="Oryza nivara">Oryza nivara</option>
-                    <option value="Oryza punctata">Oryza punctata</option>
-                    <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option>
-                    <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option>
-                    <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
-                    <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option>
-                    <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option>
-                    <option value="Physcomitrella patens">Physcomitrella patens</option>
-                    <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option>
-                    <option value="Populus trichocarpa">Populus trichocarpa</option>
-                    <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option>
-                    <option value="Prunus persica (Peach)">Prunus persica (Peach)</option>
-                    <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option>
-                    <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option>
-                    <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option>
-                    <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option>
-                    <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option>
-                    <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option>
-                    <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option>
-                    <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option>
-                    <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option>
-                    <option value="Zea mays (Maize)">Zea mays (Maize)</option>
-                </param>
-            </when>
-            <when value="Metazoa">
-                <param name="species" type="select" label="The species to use for the gene annotation"
-                    help="">
-                    <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
-                    <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option>
-                    <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
-                    <option value="Anopheles darlingi">Anopheles darlingi</option>
-                    <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option>
-                    <option value="Apis mellifera ">Apis mellifera </option>
-                    <option value="Atta cephalotes ">Atta cephalotes </option>
-                    <option value="Bombyx mori ">Bombyx mori </option>
-                    <option value="Brugia malayi ">Brugia malayi </option>
-                    <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option>
-                    <option value="Caenorhabditis briggsae ">Caenorhabditis briggsae </option>
-                    <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option>
-                    <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option>
-                    <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option>
-                    <option value="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option>
-                    <option value="Danaus plexippus ">Danaus plexippus </option>
-                    <option value="Daphnia pulex ">Daphnia pulex </option>
-                    <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option>
-                    <option value="Drosophila ananassae ">Drosophila ananassae </option>
-                    <option value="Drosophila erecta ">Drosophila erecta </option>
-                    <option value="Drosophila grimshawi ">Drosophila grimshawi </option>
-                    <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option>
-                    <option value="Drosophila mojavensis ">Drosophila mojavensis </option>
-                    <option value="Drosophila persimilis ">Drosophila persimilis </option>
-                    <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option>
-                    <option value="Drosophila sechellia ">Drosophila sechellia </option>
-                    <option value="Drosophila simulans ">Drosophila simulans </option>
-                    <option value="Drosophila virilis ">Drosophila virilis </option>
-                    <option value="Drosophila willistoni ">Drosophila willistoni </option>
-                    <option value="Drosophila yakuba ">Drosophila yakuba </option>
-                    <option value="Heliconius melpomene ">Heliconius melpomene </option>
-                    <option value="Helobdella robusta">Helobdella robusta</option>
-                    <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option>
-                    <option value="Loa loa ">Loa loa </option>
-                    <option value="Lottia gigantea">Lottia gigantea</option>
-                    <option value="Megaselia scalaris ">Megaselia scalaris </option>
-                    <option value="Melitaea cinxia">Melitaea cinxia</option>
-                    <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option>
-                    <option value="Nasonia vitripennis ">Nasonia vitripennis </option>
-                    <option value="Nematostella vectensis ">Nematostella vectensis </option>
-                    <option value="Onchocerca volvulus">Onchocerca volvulus</option>
-                    <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option>
-                    <option value="Pristionchus pacificus ">Pristionchus pacificus </option>
-                    <option value="Rhodnius prolixus">Rhodnius prolixus</option>
-                    <option value="Schistosoma mansoni ">Schistosoma mansoni </option>
-                    <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option>
-                    <option value="Strigamia maritima ">Strigamia maritima </option>
-                    <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option>
-                    <option value="Tetranychus urticae">Tetranychus urticae</option>
-                    <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option>
-                    <option value="Trichinella spiralis ">Trichinella spiralis </option>
-                    <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option>
-                    <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option>
-                </param>
-            </when>
-            <when value="Fungi">
-                <param name="species" type="select" label="The species to use for the gene annotation"
-                    help="">
-                    <option value="Ashbya gossypii">Ashbya gossypii</option>
-                    <option value="Aspergillus clavatus">Aspergillus clavatus</option>
-                    <option value="Aspergillus flavus">Aspergillus flavus</option>
-                    <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
-                    <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
-                    <option value="Aspergillus nidulans">Aspergillus nidulans</option>
-                    <option value="Aspergillus niger">Aspergillus niger</option>
-                    <option value="Aspergillus oryzae">Aspergillus oryzae</option>
-                    <option value="Aspergillus terreus">Aspergillus terreus</option>
-                    <option value="Blumeria graminis">Blumeria graminis</option>
-                    <option value="Botrytis cinerea">Botrytis cinerea</option>
-                    <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option>
-                    <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option>
-                    <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option>
-                    <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
-                    <option value="Dothistroma septosporum">Dothistroma septosporum</option>
-                    <option value="Fusarium fujikuroi">Fusarium fujikuroi</option>
-                    <option value="Fusarium graminearum">Fusarium graminearum</option>
-                    <option value="Fusarium oxysporum">Fusarium oxysporum</option>
-                    <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option>
-                    <option value="Fusarium solani">Fusarium solani</option>
-                    <option value="Fusarium verticillioides">Fusarium verticillioides</option>
-                    <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
-                    <option value="Colletotrichum graminicola">Colletotrichum graminicola</option>
-                    <option value="Komagataella pastoris">Komagataella pastoris</option>
-                    <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
-                    <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
-                    <option value="Magnaporthe poae">Magnaporthe poae</option>
-                    <option value="Melampsora larici-populina">Melampsora larici-populina</option>
-                    <option value="Neosartorya fischeri">Neosartorya fischeri</option>
-                    <option value="Neurospora crassa">Neurospora crassa</option>
-                    <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
-                    <option value="Puccinia graminis">Puccinia graminis</option>
-                    <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option>
-                    <option value="Puccinia triticina">Puccinia triticina</option>
-                    <option value="Pyrenophora teres">Pyrenophora teres</option>
-                    <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
-                    <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
-                    <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option>
-                    <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option>
-                    <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option>
-                    <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
-                    <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
-                    <option value="Sporisorium reilianum">Sporisorium reilianum</option>
-                    <option value="Trichoderma reesei">Trichoderma reesei</option>
-                    <option value="Trichoderma virens">Trichoderma virens</option>
-                    <option value="Tuber melanosporum">Tuber melanosporum</option>
-                    <option value="Ustilago maydis">Ustilago maydis</option>
-                    <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option>
-                    <option value="Verticillium dahliae">Verticillium dahliae</option>
-                    <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
-                    <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
-                </param>
-            </when>
-            <when value="Vertebrates">
-                <param name="species" type="select" label="The species to use for the gene annotation"
-                    help="">
-                    <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option>
-                    <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option>
-                    <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option>
-                    <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option>
-                    <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option>
-                    <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option>
-                    <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option>
-                    <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option>
-                    <option value="Cat (Felis catus)">Cat (Felis catus)</option>
-                    <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option>
-                    <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option>
-                    <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option>
-                    <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option>
-                    <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option>
-                    <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option>
-                    <option value="Cow (Bos taurus)">Cow (Bos taurus)</option>
-                    <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option>
-                    <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option>
-                    <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option>
-                    <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option>
-                    <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option>
-                    <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option>
-                    <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option>
-                    <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option>
-                    <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option>
-                    <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option>
-                    <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option>
-                    <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option>
-                    <option value="Horse (Equus caballus)">Horse (Equus caballus)</option>
-                    <option value="Human (Homo sapiens)">Human (Homo sapiens)</option>
-                    <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option>
-                    <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option>
-                    <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option>
-                    <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option>
-                    <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option>
-                    <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option>
-                    <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option>
-                    <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option>
-                    <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option>
-                    <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option>
-                    <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option>
-                    <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option>
-                    <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option>
-                    <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option>
-                    <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option>
-                    <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option>
-                    <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option>
-                    <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option>
-                    <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option>
-                    <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option>
-                    <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option>
-                    <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option>
-                    <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option>
-                    <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option>
-                    <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option>
-                    <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option>
-                    <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option>
-                    <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option>
-                    <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option>
-                    <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option>
-                    <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option>
-                    <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option>
-                    <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option>
-                    <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option>
-                    <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option>
-                    <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option>
-                    <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option>
-                    <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option>
-                </param>
-            </when>
-        </conditional>
         <conditional name="processing_options">
             <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
                 <option value="no" selected="True">Default Processing Options</option>
@@ -503,15 +239,53 @@
                 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
             </when>
         </conditional>
+        <conditional name="contact_options">
+            <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
+                help="Create a Galaxy workflow to save these values">
+                <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
+                <option value="yes">Specify Contact Information</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="contact_first_name" type="text" value="" label="Contact first name.">
+                    <validator type="regex" message="">\S+.*</validator>
+                </param>
+                <param name="contact_last_name" type="text" value="" label="Contact last name.">
+                    <validator type="regex" message="">\S+.*</validator>
+                </param>
+                <param name="contact_email" type="text" value="" label="Contact e-mail.">
+                    <validator type="regex" message="">\S+@\S+</validator>
+                </param>
+                <param name="contact_address" type="text" value="" label="Contact address.">
+                    <validator type="regex" message="">\S+.*</validator>
+                </param>
+                <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
+                </param>
+                <param name="organization_name" type="text" value="" label="Organization name.">
+                    <validator type="regex" message="">\S+.*</validator>
+                </param>
+                <param name="organization_email" type="text" value="" label="Organization e-mail.">
+                    <validator type="regex" message="">\S+@\S+</validator>
+                </param>
+                <param name="organization_address" type="text" value="" label="Organization address.">
+                    <validator type="regex" message="">\S+.*</validator>
+                </param>
+                <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
+                </param>
+            </when>
+        </conditional>
+
+        <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
         <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
             <option value="zip">Zip File for import to Desktop App</option>
             <option value="mzidentML" selected="True">mzidentML File</option>
-            <option value="3" >PSM Report</option>
-            <option value="4" >Peptide Phosphorylation Report</option>
-            <option value="5" >Peptide Report</option>
-            <option value="6" >Protein Phosphorylation Report</option>
-            <option value="7" >Protein Report</option>
+            <option value="3">PSM Report</option>
+            <option value="8">Extended PSM Report</option>
             <option value="2">PSM Phosphorylation Report</option>
+            <option value="5">Peptide Report</option>
+            <option value="4">Peptide Phosphorylation Report</option>
+            <option value="7">Protein Report</option>
+            <option value="6">Protein Phosphorylation Report</option>
             <option value="0">Certificate of Analysis</option>
             <option value="1">Hierarchical Report</option>
             <option value="cps">CPS file</option>
@@ -541,6 +315,9 @@
         <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
             <filter>'3' in outputs</filter>
         </data>
+        <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
+            <filter>'8' in outputs</filter>
+        </data>
         <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
             <filter>'4' in outputs</filter>
         </data>
diff -r 2f8e9d0351a8 -r ffed32e397cb searchgui.xml
--- a/searchgui.xml	Fri Jun 10 09:57:31 2016 -0400
+++ b/searchgui.xml	Wed Jan 11 13:06:06 2017 -0500
@@ -7,7 +7,9 @@
     </macros>
     <requirements>
         <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
+        <!-- 
         <environment_variable name="LC_ALL" action="set_to">C</environment_variable>        
+        -->
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -16,21 +18,25 @@
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $temp_stderr = "searchgui_stderr"
+        #set $bin_dir = "bin"
 
         mkdir output;
         mkdir output_reports;
         cwd=`pwd`;
         export HOME=\$cwd;
 
+        ## echo the search engines to run
+        echo "$engines";
+        echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
+
         ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
         echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
 
-        cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
-        tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
-
         #for $mgf in $peak_lists:
             #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
             ln -s -f '${mgf}' '${input_name}';
+            #set $encoded_id = $__app__.security.encode_id($mgf.id)
+            echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
         #end for
         ##ln -s "${input_database}" input_database.fasta;
         cp "${input_database}" input_database.fasta;
@@ -40,7 +46,7 @@
         ###########################################
         #if $create_decoy:
             echo "Creating decoy database.";
-            java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
+            searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
             ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
@@ -49,8 +55,8 @@
         #####################################################
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
-
-        (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
+        (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
+            --exec_dir="\$cwd/${bin_dir}"
             -out SEARCHGUI_IdentificationParameters.par
 
             @GENERAL_PARAMETERS@
@@ -196,6 +202,7 @@
                 -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}
             #end if
             *#
  
@@ -245,15 +252,16 @@
                 #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
                     -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
                     -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
-                    -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}
+
+                    -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}
 
 
-                     #if $comet.comet_spectrum.comet_remove_prec == "1"
-                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                     #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
+                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                      #end if
                      
-                     #if $comet.comet_spectrum.comet_remove_prec == "2"
-                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                     #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
+                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
                      #end if
                      
                     -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
@@ -279,13 +287,44 @@
                 #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}
+                #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}
+            #end if
+
+            #if $novor.novor_advanced == "yes"
+                -novor_fragmentation ${novor.novor_fragmentation}
+                -novor_mass_analyzer ${novor.novor_mass_analyzer}
+            #end if
+
         2> $temp_stderr)
         &&
 
         ################
         ## Search CLI ##
         ################
-        (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI 
+        (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 
+            --exec_dir="\$cwd/${bin_dir}"
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
@@ -355,6 +394,18 @@
                 -andromeda 0
             #end if
 
+            #if 'Novor' in $engines_list:
+                -novor 1
+            #else
+                -novor 0
+            #end if
+
+            #if 'DirecTag' in $engines_list:
+                -directag 1
+            #else
+                -directag 0
+            #end if
+
             ## single zip file
             -output_option 0
 
@@ -396,19 +447,26 @@
         <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>
-            <!-- Not working in tests
-            <option value="MyriMatch">MyriMatch</option> 
-            <option value="MS_Amanda">MS_Amanda</option>
-            -->
+
             <option value="MSGF" selected="True">MS-GF+</option>
             <option value="OMSSA" selected="True">OMSSA</option>
             <option value="Comet">Comet</option>
             <!-- 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>
 
@@ -439,7 +497,7 @@
 
             <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>
+            </when>
         </conditional>
 
 
@@ -470,7 +528,7 @@
                 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
                     label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 
                 <param name="xtandem_evalue" help="Highest value for recorded peptides"
-                    label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
+                    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"
@@ -867,6 +925,7 @@
                 <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>
         -->
@@ -891,20 +950,22 @@
                             label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
                         <param name="comet_min_peak_int"  type="float" value="0.0"
                             label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
-                        <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
-                            <option value="0"  selected="True" >off</option>
-                            <option value="1">on</option>
-                            <option value="2">as expected for ETD/ECD spectra</option>
-                        </param>
-                        <when value="0" />
-                        <when value="1">
-                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
-                                label="Comet: Remove Precursor Tolerance" />
-                        </when>
-                        <when value="2">
-                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
-                                label="Comet: Remove Precursor Tolerance" />
-                        </when>
+                        <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"
@@ -964,6 +1025,59 @@
                 </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>
+                <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>
+
     </inputs>
     <outputs>
         <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
diff -r 2f8e9d0351a8 -r ffed32e397cb tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jun 10 09:57:31 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="searchgui" version="2.9">
-        <repository changeset_revision="ad67fd4127ae" name="package_searchgui_2_9" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="peptide_shaker" version="1.11">
-        <repository changeset_revision="7c812d11f172" name="package_peptideshaker_1_11" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>