diff peptide_shaker.xml @ 20:2cafc729b2ae draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
author iracooke
date Sun, 31 May 2015 09:05:57 -0400
parents a5f9b959d5d1
children dfaea053e32f
line wrap: on
line diff
--- a/peptide_shaker.xml	Wed Jun 25 11:50:38 2014 -0400
+++ b/peptide_shaker.xml	Sun May 31 09:05:57 2015 -0400
@@ -1,211 +1,44 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0">
     <description>
-        Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
+        Perform protein identification using various search engines based on results from SearchGUI
     </description>
     <requirements>
-        <requirement type="package" version="0.31.4">peptide_shaker</requirement>
-        <requirement type="package" version="1.19.5">searchgui</requirement>
-        <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
+        <requirement type="package" version="0.38">peptide_shaker</requirement>
     </requirements>
-    <stdio>
-        <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"/>
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="stdio" />
     <command>
-
+<![CDATA[
         #from datetime import datetime
         #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 = 'macs2_stderr'
+        #set $temp_stderr = "peptideshaker_stderr"
 
-        mkdir output;
         mkdir output_reports;
         cwd=`pwd`;
-        #for $mgf in $peak_lists:
-            #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
-            ln -s '${mgf}' '${input_name}';
-        #end for
-        ##ln -s "${input_database}" input_database.fasta;
-        cp "${input_database}" input_database.fasta;
 
-        ###########################################
-        ####       Creating decoy database     ####
-        ###########################################
-        #if $create_decoy:
-            echo "Creating decoy database.";
-            java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
-            rm input_database.fasta;
-            cp input_database_concatenated_target_decoy.fasta input_database.fasta;
-            ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
-        #end if
-
-        #####################################################
-        ## generate IdentificationParameters for SearchGUI ##
-        #####################################################
-
-        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
-            -out SEARCHGUI_IdentificationParameters.parameters
-            -prec_ppm "${precursor_ion_tol_units}"
-            -prec_tol "${precursor_ion_tol}"
-            -frag_tol "${fragment_tol}"
-            -enzyme "${enzyme}"
-            #set $fixed_mods_str = $fixed_modifications or ''
-            #set $variable_mods_str = $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}"
-            -mc "${missed_cleavages}"
-            -fi "${forward_ion}"
-            -ri "${reverse_ion}"
-            -db input_database.fasta
-
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-
-                    -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
-                    -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
-                    -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
-                    -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
-                    -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
-
-                    #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
-                        -xtandem_refine 1
-                        -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
-                        -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
-                        -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
-                        -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
-                        -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
-                    #end if
-                #end if
-
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa_hitlist_length ${advanced.omssa.hitlist_length}
-                    -omssa_remove_prec ${advanced.omssa.remove_precursor}
-                    -omssa_scale_prec ${advanced.omssa.scale_precursor}
-                    -omssa_estimate_charge ${advanced.omssa.estimate_charge}
-                #end if
-
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf_decoy ${advanced.msgf.msgf_decoy}
-                    -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
-                    -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
-                    -msgf_termini ${advanced.msgf.msgf_termini}
-                    -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
-                #end if
-
-                ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                ##end if
-
-            #end if
-
-        2> $temp_stderr)
-        &amp;&amp;
-
-        ################
-        ## Search CLI ##
-        ################
-        (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 
-            -temp_folder `pwd`
-            -spectrum_files \$cwd
-            -output_folder \$cwd/output
-            -id_params SEARCHGUI_IdentificationParameters.parameters
-
-            -threads "\${GALAXY_SLOTS:-12}"
-            -correct_titles "${correct_titles}"
-            $missing_titles
-            -mgf_splitting "${mgf_splitting}"
-            -mgf_spectrum_count "${mgf_spectrum_count}"
-
-            ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
-            ## the tree is generated afterwards in PeptideShaker
-            -protein_index 0
-
-            ##-makeblastdb_folder \$BLAST_ROOT_DIR
-
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-                    -xtandem 1
-                #else
-                    -xtandem 0
-                #end if
-
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa 1
-                #else
-                    -omssa 0
-                #end if
-
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf 1
-                #else
-                    -msgf 0
-                #end if
-
-                #if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                    -ms_amanda 1
-                #else
-                    -ms_amanda 0
-                #end if
-
-            #else
-                -ms_amanda 0
-            #end if
-            
-        2>> $temp_stderr)
-        &amp;&amp;
-
-        #########################################################
-        ## generate IdentificationParameters for PeptideShaker ##
-        #########################################################
-        (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
-            -out PEPTIDESHAKER_IdentificationParameters.parameters
-            -prec_ppm "${precursor_ion_tol_units}"
-            -prec_tol "${precursor_ion_tol}"
-            -frag_tol "${fragment_tol}"
-            -enzyme "${enzyme}"
-            #set $fixed_mods_str = $fixed_modifications or ''
-            #set $variable_mods_str = $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
-            -mc $missed_cleavages
-            -fi $forward_ion
-            -ri $reverse_ion
-            -db input_database.fasta
-
-        2>> $temp_stderr)
-        &amp;&amp;
-
+        ln -s '$searchgui_input' searchgui_input.zip &&
         ######################
         ## PeptideShakerCLI ##
         ######################
         (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
-            -temp_folder `pwd`
-            -experiment '${exp_str}'
-            -sample '${samp_str}'
+            -temp_folder \$cwd/PeptideShakerCLI
+            -experiment '$exp_str'
+            -sample '$samp_str'
             -replicate 1
-            -spectrum_files \$cwd
-            -identification_files \$cwd/output
-            -out \$cwd/peptide_shaker_output.cps
-            -id_params PEPTIDESHAKER_IdentificationParameters.parameters
+            -identification_files \$cwd/searchgui_input.zip
+            -out \$cwd/peptideshaker_output.cps
+            -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:
@@ -229,132 +62,107 @@
                 -max_peptide_length "${filtering_options.max_peptide_length}"
                 -max_precursor_error "${filtering_options.max_precursor_error}"
                 -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
-                -max_xtandem_e "${filtering_options.max_xtandem_e}"
-                -max_omssa_e "${filtering_options.max_omssa_e}"
-                -max_mascot_e "${filtering_options.max_mascot_e}"
+                ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
+                ##-max_omssa_e "${filtering_options.max_omssa_e}"
+                ##-max_mascot_e "${filtering_options.max_mascot_e}"
                 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
             #end if
 
         2>> $temp_stderr)
-        &amp;&amp;
+
+        &&
+
+        echo "Running Reports";
 
         ##################################
         ## PeptideShaker Report options ##
         ##################################
-        (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
-            -temp_folder `pwd`
-            -in \$cwd/peptide_shaker_output.cps
-            -out_reports \$cwd/output_reports
-            #set $cleaned_list = str($outputs).split(',')
-            #if 'cps' in $cleaned_list:
-                #silent $cleaned_list.remove('cps')
-            #end if
-            #if 'mzidentML' in $cleaned_list:
-                #silent $cleaned_list.remove('mzidentML')
-            #end if
-            -reports #echo ','.join($cleaned_list)#
-
-        2>> $temp_stderr)
-        &amp;&amp;
 
         #if 'mzidentML' in str($outputs).split(','):
-            java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
-                -in \$cwd/peptide_shaker_output.cps
+            echo "Generating mzIdentML";
+            (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
+                -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'
-                ;
+                -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"
+            2>> $temp_stderr) 
+            &&
         #end if
+
+        ## Generate Reports if the user has selected one of the 8 additional reports
+        ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 
+        ## 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 \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
+                -temp_folder \$cwd/ReportCLI
+                -in \$cwd/peptideshaker_output.zip
+                -out_reports \$cwd/output_reports
+                #set $cleaned_list = str($outputs).split(',')
+                #if 'cps' in $cleaned_list:
+                    #silent $cleaned_list.remove('cps')
+                #end if
+                #if 'mzidentML' in $cleaned_list:
+                    #silent $cleaned_list.remove('mzidentML')
+                #end if
+                #if 'zip' in $cleaned_list:
+                    #silent $cleaned_list.remove('zip')
+                #end if
+                ## Only numbers are left over. These corresponds to different reports.
+                -reports #echo ','.join($cleaned_list)#
+
+            2>> $temp_stderr)
+            &&
+        #end if
+
+
         #if '0' in str($outputs).split(','):
-            find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
-            ;
-        #end if
-        #if '2' in str($outputs).split(','):
-            find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
-            ;
-        #end if
-        #if '3' in str($outputs).split(','):
-            find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
-            ;
-        #end if
-        #if '4' in str($outputs).split(','):
-            find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
+            find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
             ;
         #end if
         #if '1' in str($outputs).split(','):
             find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
             ;
         #end if
+        #if '2' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
+            ;
+        #end if
+        #if '3' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
+            ;
+        #end if
+        #if '4' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
+            ;
+        #end if
+        #if '5' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
+            ;
+        #end if
+        #if '6' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
+            ;
+        #end if
+        #if '7' in str($outputs).split(','):
+            find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
+            ;
+        #end if
 
         exit_code_for_galaxy=\$?;
-        cat $temp_stderr 2&gt;&amp;1;
+        cat $temp_stderr 2>&1;
         (exit \$exit_code_for_galaxy)
 
+]]>
     </command>
     <inputs>
-        <param format="fasta" name="input_database" type="data" label="Protein Database"
-            help="Select FASTA database from history"/>
-
-        <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" />
-
-        <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
-            help="Select appropriate MGF dataset(s) from history" />
-        <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="0">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="No enzyme">No enzyme</option>
-            <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>
-        </param>
-
-        <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" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" 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"/>
+        <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results"
+            help="SearchGUI Results from History"/>
 
         <conditional name="species_type">
             <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
@@ -370,14 +178,20 @@
                 <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>
@@ -385,7 +199,12 @@
                     <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>
@@ -395,77 +214,102 @@
             <when value="Plants">
                 <param name="species" type="select" label="The species to use for the gene annotation"
                     help="">
-                    <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
-                    <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
-                    <option value="Brachypodium distachyon">Brachypodium distachyon</option>
-                    <option value="Brassica rapa genes">Brassica rapa genes</option>
-                    <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>
-                    <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option>
-                    <option value="Glycine max">Glycine max</option>
-                    <option value="Hordeum vulgare">Hordeum vulgare</option>
-                    <option value="Medicago truncatula">Medicago truncatula</option>
-                    <option value="Musa acuminata">Musa acuminata</option>
+                    <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 glaberrima">Oryza glaberrima</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">Oryza sativa</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="Selaginella moellendorffii">Selaginella moellendorffii</option>
-                    <option value="Setaria italica">Setaria italica</option>
-                    <option value="Solanum lycopersicum">Solanum lycopersicum</option>
-                    <option value="Solanum tuberosum">Solanum tuberosum</option>
-                    <option value="Sorghum bicolor">Sorghum bicolor</option>
-                    <option value="Vitis vinifera">Vitis vinifera</option>
-                    <option value="Zea mays">Zea mays</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">Aedes aegypti</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">Anopheles gambiae</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">Culex quinquefasciatus</option>
-                    <option value="Danaus plexippus">Danaus plexippus</option>
-                    <option value="Daphnia pulex">Daphnia pulex</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">Drosophila melanogaster</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="Ixodes scapularis">Ixodes scapularis</option>
-                    <option value="Loa loa">Loa loa</option>
-                    <option value="Megaselia scalaris">Megaselia scalaris</option>
-                    <option value="Nasonia vitripennis">Nasonia vitripennis</option>
-                    <option value="Nematostella vectensis">Nematostella vectensis</option>
-                    <option value="Pediculus humanus">Pediculus humanus</option>
-                    <option value="Pristionchus pacificus">Pristionchus pacificus</option>
-                    <option value="Schistosoma mansoni">Schistosoma mansoni</option>
-                    <option value="Strigamia maritima">Strigamia maritima</option>
-                    <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option>
-                    <option value="Tribolium castaneum">Tribolium castaneum</option>
-                    <option value="Trichinella spiralis">Trichinella spiralis</option>
-                    <option value="Trichoplax adhaerens">Trichoplax adhaerens</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">
@@ -480,27 +324,38 @@
                     <option value="Aspergillus niger">Aspergillus niger</option>
                     <option value="Aspergillus oryzae">Aspergillus oryzae</option>
                     <option value="Aspergillus terreus">Aspergillus terreus</option>
-                    <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</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="Gibberella moniliformis">Gibberella moniliformis</option>
-                    <option value="Gibberella zeae">Gibberella zeae</option>
-                    <option value="Glomerella graminicola">Glomerella graminicola</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="Nectria haematococca">Nectria haematococca</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>
@@ -508,6 +363,8 @@
                     <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>
@@ -515,179 +372,77 @@
             <when value="Vertebrates">
                 <param name="species" type="select" label="The species to use for the gene annotation"
                     help="">
-                    <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
-                    <option value="Anolis carolinensis">Anolis carolinensis</option>
-                    <option value="Bos taurus">Bos taurus</option>
-                    <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
-                    <option value="Callithrix jacchus">Callithrix jacchus</option>
-                    <option value="Canis familiaris">Canis familiaris</option>
-                    <option value="Cavia porcellus">Cavia porcellus</option>
-                    <option value="Choloepus hoffmanni">Choloepus hoffmanni</option>
-                    <option value="Ciona intestinalis">Ciona intestinalis</option>
-                    <option value="Ciona savignyi">Ciona savignyi</option>
-                    <option value="Danio rerio">Danio rerio</option>
-                    <option value="Dasypus novemcinctus">Dasypus novemcinctus</option>
-                    <option value="Dipodomys ordii">Dipodomys ordii</option>
-                    <option value="Drosophila melanogaster">Drosophila melanogaster</option>
-                    <option value="Echinops telfairi">Echinops telfairi</option>
-                    <option value="Equus caballus">Equus caballus</option>
-                    <option value="Erinaceus europaeus">Erinaceus europaeus</option>
-                    <option value="Felis catus">Felis catus</option>
-                    <option value="Gallus gallus">Gallus gallus</option>
-                    <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option>
-                    <option value="Gorilla gorilla">Gorilla gorilla</option>
-                    <option value="Homo sapiens">Homo sapiens</option>
-                    <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option>
-                    <option value="Latimeria chalumnae">Latimeria chalumnae</option>
-                    <option value="Loxodonta africana">Loxodonta africana</option>
-                    <option value="Macaca mulatta">Macaca mulatta</option>
-                    <option value="Macropus eugenii">Macropus eugenii</option>
-                    <option value="Meleagris gallopavo">Meleagris gallopavo</option>
-                    <option value="Microcebus murinus">Microcebus murinus</option>
-                    <option value="Monodelphis domestica">Monodelphis domestica</option>
-                    <option value="Mus musculus">Mus musculus</option>
-                    <option value="Mustela putorius furo">Mustela putorius furo</option>
-                    <option value="Myotis lucifugus">Myotis lucifugus</option>
-                    <option value="Nomascus leucogenys">Nomascus leucogenys</option>
-                    <option value="Ochotona princeps">Ochotona princeps</option>
-                    <option value="Oreochromis niloticus">Oreochromis niloticus</option>
-                    <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
-                    <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
-                    <option value="Oryzias latipes">Oryzias latipes</option>
-                    <option value="Otolemur garnettii">Otolemur garnettii</option>
-                    <option value="Pan troglodytes">Pan troglodytes</option>
-                    <option value="Petromyzon marinus">Petromyzon marinus</option>
-                    <option value="Pelodiscus sinensis">Pelodiscus sinensis</option>
-                    <option value="Pongo abelii">Pongo abelii</option>
-                    <option value="Procavia capensis">Procavia capensis</option>
-                    <option value="Pteropus vampyrus">Pteropus vampyrus</option>
-                    <option value="Rattus norvegicus">Rattus norvegicus</option>
-                    <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
-                    <option value="Sarcophilus harrisii">Sarcophilus harrisii</option>
-                    <option value="Sorex araneus">Sorex araneus</option>
-                    <option value="Sus scrofa">Sus scrofa</option>
-                    <option value="Taeniopygia guttata">Taeniopygia guttata</option>
-                    <option value="Takifugu rubripes">Takifugu rubripes</option>
-                    <option value="Tarsius syrichta">Tarsius syrichta</option>
-                    <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option>
-                    <option value="Tupaia belangeri">Tupaia belangeri</option>
-                    <option value="Tursiops truncatus">Tursiops truncatus</option>
-                    <option value="Vicugna pacos">Vicugna pacos</option>
-                    <option value="Xenopus tropicalis">Xenopus tropicalis</option>
-                    <option value="Xiphophorus maculatus">Xiphophorus maculatus</option>
+                    <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>
-
-        <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>
-        <conditional name="advanced">
-            <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
-                <option value="basic" selected="True">Basic</option>
-                <option value="advanced">Advanced</option>
-            </param>
-            <when value="basic" />
-            <when value="advanced">
-                <conditional name="xtandem">
-                    <param name="xtandem_selector" type="select" label="Run X!Tandem search">
-                        <option value="yes" selected="True">Search with X!Tandem</option>
-                        <option value="no">No X!Tandem search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
-                        <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
-                        <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                        <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                        <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
-
-                        <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" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
-                                <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
-                                <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
-                                <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
-                                <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
-                            </when>
-                        </conditional>
-                    </when>
-                </conditional>
-
-                <conditional name="omssa">
-                    <param name="omssa_selector" type="select" label="Run OMSSA search">
-                        <option value="yes" selected="True">Search with OMSSA</option>
-                        <option value="no">No OMSSA search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-                        <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                        <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-                        <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-                    </when>
-                </conditional>
-
-                <conditional name="msgf">
-                    <param name="msgf_selector" type="select" label="Run MSGF search">
-                        <option value="yes" selected="True">Search with MSGF</option>
-                        <option value="no">No MSGF search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="msgf_decoy" label="Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
-                        <param name="msgf_min_pep_length" label="Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
-                        <param name="msgf_max_pep_length" label="Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
-                        <param name="msgf_termini" label="Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
-                            <option value="0">0 (ie non-specific cleavage)</option>
-                            <option value="1">1 (ie semi-tryptic cleavage)</option>
-                            <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
-                        </param>
-                        <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
-                    </when>
-                </conditional>
-
-                <conditional name="ms_amanda">
-                    <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
-                        <option value="yes">Search with MS Amanda</option>
-                        <option value="no" selected="True">No MS Amanda search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-            </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>
@@ -698,7 +453,7 @@
                 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
                 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
-                <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
+                <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
                     help="default 95%: '95.0'" />
                 <conditional name="ptm_score">
                     <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
@@ -719,80 +474,111 @@
             <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
                 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
                 <option value="no" selected="True">Default Filtering Options</option>
-                <option value="yes">Advanced Processing Options</option>
+                <option value="yes">Advanced Filtering Options</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
-                <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
-                <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" />
+                <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
+                <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
+                <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
+                    help="Next option specifies units (Da or ppm)" />
                 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
                     <option value="0">ppm</option>
                     <option value="1">Daltons</option>
                 </param>
-                <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
-                <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
-                <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" />
+                <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
+                <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
+                <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
                 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
             </when>
         </conditional>
-
         <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" selected="True">Peptide Report</option>
-            <option value="4" selected="True">Protein Report</option>
-            <option value="2">PSM Report</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="2">PSM Phosphorylation Report</option>
             <option value="0">Certificate of Analysis</option>
             <option value="1">Hierarchical Report</option>
             <option value="cps">CPS file</option>
             <validator type="no_options" message="Please select at least one output file" />
         </param>
+
     </inputs>
     <outputs>
         <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
             <filter>'mzidentML' in outputs</filter>
         </data>
-        <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
+        <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
             <filter>'cps' in outputs</filter>
         </data>
+        <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
+            <filter>'zip' in outputs</filter>
+        </data>
         <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
             <filter>'0' in outputs</filter>
         </data>
-        <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
+        <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
+            <filter>'1' in outputs</filter>
+        </data>
+        <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
             <filter>'2' in outputs</filter>
         </data>
-        <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
+        <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
             <filter>'3' in outputs</filter>
         </data>
-        <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
+        <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
             <filter>'4' in outputs</filter>
         </data>
-        <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
-            <filter>'1' in outputs</filter>
+        <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
+            <filter>'5' in outputs</filter>
+        </data>
+        <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
+            <filter>'6' in outputs</filter>
+        </data>
+        <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
+            <filter>'7' in outputs</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="input_database" value="tinydb.fasta"/>
-            <param name="peak_lists" value="tinyspectra.mgf"/>
-            <param name="precursor_ion_tol" value="100"/>
-            <param name="fixed_modifications" value="carbamidomethyl c"/>
-            <param name="variable_modifications" value="oxidation of m"/>
-            <param name="min_charge" value="1"/>
-            <param name="max_charge" value="3"/>
-            <param name="advanced_type_selector" value="advanced"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
-            <!--param name="xtandem_selector" value="no"/>-->
-            <param name="xtandem_selector" value="yes"/>
-            <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
-
-            <param name="omssa_selector" value="no"/>
-            <param name="msgf_selector" value="yes"/>
-            <param name="ms_amanda_selector" value="no"/>
-            
-            <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> 
+            <param name="outputs" value="zip,cps,3"/>
+            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />
+            <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" />
+            <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="species_type_selector" value="no_species_type"/>
+            <param name="processing_options_selector" value="no"/>
+            <param name="filtering_options_selector" value="yes"/>
+            <param name="min_peptide_length" value="1"/>
+            <param name="outputs" value="0,1,2,3,4,5,6,7"/>
+            <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/>
+            <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
+            <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
+            <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
+            <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
+            <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
+            <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
+            <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="species_type_selector" value="Vertebrates"/>
+            <param name="species" value="Human (Homo sapiens)"/>
+            <param name="processing_options_selector" value="no"/>
+            <param name="filtering_options_selector" value="yes"/>
+            <param name="min_peptide_length" value="1"/>
+            <param name="outputs" value="5"/>
+            <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" />
         </test>
     </tests>
     <help>
@@ -814,8 +600,8 @@
 ----------
 
 * Protein(s):                Protein(s) to which the peptide can be attached
-* Sequence:	                Sequence of the peptide
-* Variable Modifications:	The variable modifications
+* Sequence:                  Sequence of the peptide
+* Variable Modifications:   The variable modifications
 * D-score:	                D-score for variable PTM localization
 * probabilistic PTM score:	The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
 * Localization Confidence:	The confidence in variable PTM localization.
@@ -945,8 +731,6 @@
 * Validation:	Indicates the validation level of the protein group.
 
 
-
-
 ------
 
 **Citation**
@@ -955,4 +739,5 @@
 
 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
     </help>
+    <expand macro="citations" />
 </tool>