Mercurial > repos > galaxyp > peptideshaker
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 |
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--- 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> $temp_stderr) - && - - ################ - ## Search CLI ## - ################ - (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI - -temp_folder `pwd` - -spectrum_files \$cwd - -output_folder \$cwd/output - -id_params SEARCHGUI_IdentificationParameters.parameters - - -threads "\${GALAXY_SLOTS:-12}" - -correct_titles "${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>> $temp_stderr) - && - - ######################################################### - ## generate IdentificationParameters for PeptideShaker ## - ######################################################### - (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI - -out PEPTIDESHAKER_IdentificationParameters.parameters - -prec_ppm "${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>> $temp_stderr) - && - + ln -s '$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) - && + + && + + 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>> $temp_stderr) - && #if 'mzidentML' in str($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>&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>