Mercurial > repos > galaxyp > peptideshaker
view peptide_shaker.xml @ 18:a5f9b959d5d1 draft
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| author | iracooke |
|---|---|
| date | Wed, 25 Jun 2014 11:49:45 -0400 |
| parents | |
| children | 2cafc729b2ae |
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<tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0"> <description> Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker. </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>--> </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> <command> #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' 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>> $temp_stderr) && ###################### ## PeptideShakerCLI ## ###################### (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` -experiment '${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 ##Optional gene annotation parameter #if $species_type.species_type_selector != 'no_species_type': -species_type "${species_type.species_type_selector}" -species "${species_type.species}" #end if ##Optional processing parameters: #if $processing_options.processing_options_selector == "yes" -protein_FDR "${processing_options.protein_fdr}" -peptide_FDR "${processing_options.peptide_fdr}" -psm_FDR "${processing_options.psm_fdr}" -ptm_score "${processing_options.ptm_score.ptm_score_selector}" #if $processing_options.ptm_score.ptm_score_selector == 1 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" #if str($processing_options.ptm_score.ptm_threshold) != '' -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" #end if #end if -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" #end if ##Optional filtering parameters: #if $filtering_options.filtering_options_selector == "yes": -min_peptide_length "${filtering_options.min_peptide_length}" -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}" -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" #end if 2>> $temp_stderr) && ################################## ## 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 -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' ; #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 "$0" "proteins.txt"' {} \; ; #end if #if '1' in str($outputs).split(','): find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; ; #end if exit_code_for_galaxy=\$?; 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"/> <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results"> <option value="Fungi">Fungi</option> <option value="Plants">Plants</option> <option value="Metazoa">Metazoa</option> <option value="Vertebrates">Vertebrates</option> <option value="Protists">Protists</option> <option value="no_species_type" selected="true">No species restriction</option> </param> <when value="Protists"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="Albugo laibachii">Albugo laibachii</option> <option value="Dictyostelium discoideum">Dictyostelium discoideum</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="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option> <option value="Phytophthora infestans">Phytophthora infestans</option> <option value="Phytophthora ramorum">Phytophthora ramorum</option> <option value="Phytophthora sojae">Phytophthora sojae</option> <option value="Plasmodium berghei">Plasmodium berghei</option> <option value="Plasmodium chabaudi">Plasmodium chabaudi</option> <option value="Plasmodium falciparum">Plasmodium falciparum</option> <option value="Plasmodium knowlesi">Plasmodium knowlesi</option> <option value="Plasmodium vivax">Plasmodium vivax</option> <option value="Pythium ultimum">Pythium ultimum</option> <option value="Tetrahymena thermophila">Tetrahymena thermophila</option> <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option> <option value="Toxoplasma gondii">Toxoplasma gondii</option> <option value="Trypanosoma brucei">Trypanosoma brucei</option> </param> </when> <when value="Plants"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="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="Oryza brachyantha">Oryza brachyantha</option> <option value="Oryza glaberrima">Oryza glaberrima</option> <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option> <option value="Oryza sativa">Oryza sativa</option> <option value="Physcomitrella patens">Physcomitrella patens</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> </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="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> </param> </when> <when value="Fungi"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="Ashbya gossypii">Ashbya gossypii</option> <option value="Aspergillus clavatus">Aspergillus clavatus</option> <option value="Aspergillus flavus">Aspergillus flavus</option> <option value="Aspergillus fumigatus">Aspergillus fumigatus</option> <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option> <option value="Aspergillus nidulans">Aspergillus nidulans</option> <option value="Aspergillus niger">Aspergillus niger</option> <option value="Aspergillus oryzae">Aspergillus oryzae</option> <option value="Aspergillus terreus">Aspergillus terreus</option> <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option> <option value="Cryptococcus neoformans">Cryptococcus neoformans</option> <option value="Fusarium oxysporum">Fusarium oxysporum</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="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 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 pombe">Schizosaccharomyces pombe</option> <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option> <option value="Sporisorium reilianum">Sporisorium reilianum</option> <option value="Trichoderma reesei">Trichoderma reesei</option> <option value="Trichoderma virens">Trichoderma virens</option> <option value="Tuber melanosporum">Tuber melanosporum</option> <option value="Ustilago maydis">Ustilago maydis</option> <option value="Yarrowia lipolytica">Yarrowia lipolytica</option> <option value="Zymoseptoria tritici">Zymoseptoria tritici</option> </param> </when> <when value="Vertebrates"> <param name="species" type="select" label="The species to use for the gene annotation" help=""> <option value="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> </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> <option value="yes">Advanced Processing Options</option> </param> <when value="no" /> <when value="yes"> <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" 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"> <option value="0" selected="True">A-score</option> <option value="1">PhosphoRS</option> </param> <when value="0" /> <when value="1"> <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float" help="Automatic mode will be used if not set" /> </when> </conditional> <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> </when> </conditional> <conditional name="filtering_options"> <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> </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="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="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="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="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 ${on_string}: CPS file"> <filter>'cps' in outputs</filter> </data> <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${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 ${on_string}: PSM Report"> <filter>'2' in outputs</filter> </data> <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> <filter>'3' in outputs</filter> </data> <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> <filter>'4' in outputs</filter> </data> <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> <filter>'1' in outputs</filter> </data> </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="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" /> </test> </tests> <help> **What it does** Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. https://code.google.com/p/peptide-shaker/ https://code.google.com/p/searchgui/ ---- Reports ======= PSM Report ---------- * Protein(s): Protein(s) to which the peptide can be attached * 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. * Fixed Modifications: The fixed modifications. * Spectrum File: The spectrum file. * Spectrum Title: The title of the spectrum. * Spectrum Scan Number: The spectrum scan number. * RT: Retention time * m/z: Measured m/z * Measured Charge: The charge as given in the spectrum file. * Identification Charge: The charge as inferred by the search engine. * Theoretical Mass: The theoretical mass of the peptide. * Isotope Number: The isotope number targetted by the instrument. * Precursor m/z Error: The precursor m/z matching error. * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). * Confidence: Confidence in percent associated to the retained PSM. * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. Protein Report -------------- * Main Accession: Main accession of the protein group. * Description: Description of the protein designed by the main accession. * Gene Name: The gene names of the Ensembl gene ID associated to the main accession. * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession. * PI: Protein Inference status of the protein group. * Secondary Accessions: Other accessions in the protein group (alphabetical order). * Protein Group: The complete protein group (alphabetical order). * #Peptides: Total number of peptides. * #Validated Peptides: Number of validated peptides. * #Unique: Total number of peptides unique to this protein group. * #PSMs: Number of PSMs * #Validated PSMs: Number of validated PSMs * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. * MW (kDa): Molecular Weight. * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized. * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized. * Score: Score of the protein group. * Confidence: Confidence in percent associated to the protein group. * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. Peptide Report -------------- * Protein(s): Protein(s) to which this peptide can be attached. * AAs Before: The amino-acids before the sequence. * Sequence: Sequence of the peptide. * AAs After: The amino-acids after the sequence. * Modified Sequence: The peptide sequence annotated with variable modifications. * Variable Modifications: The variable modifications. * Localization Confidence: The confidence in PTMs localization. * Fixed Modifications: The fixed modifications. * #Validated PSMs: Number of validated PSMs. * #PSMs: Number of PSMs. * Score: Score of the peptide. * Confidence: Confidence in percent associated to the peptide. * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. Hierachical Report ------------------ * Main Accession: Main accession of the protein group. * Description: Description of the protein designed by the main accession. * PI: Protein Inference status of the protein group. * Secondary Accessions: Other accessions in the protein group (alphabetical order). * Protein Group: The complete protein group (alphabetical order). * #Peptides: Total number of peptides. * #Validated Peptides: Number of validated peptides. * #Unique: Total number of peptides unique to this protein group. * #PSMs: Number of PSMs * #Validated PSMs: Number of validated PSMs * Coverage (%): Sequence coverage in percent of the protein designed by the main accession. * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings. * MW (kDa): Molecular Weight. * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF) * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI) * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized. * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized. * Score: Score of the protein group. * Confidence: Confidence in percent associated to the protein group. * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. * Protein(s): Protein(s) to which this peptide can be attached. * AAs Before: The amino-acids before the sequence. * Sequence: Sequence of the peptide. * AAs After: The amino-acids after the sequence. * Variable Modifications: The variable modifications. * Localization Confidence: The confidence in PTMs localization. * Fixed Modifications: The fixed modifications. * #Validated PSMs: Number of validated PSMs. * #PSMs: Number of PSMs. * Score: Score of the peptide. * Confidence: Confidence in percent associated to the peptide. * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. * Protein(s): Protein(s) to which the peptide can be attached. * Sequence: Sequence of the peptide. * Modified Sequence: The peptide sequence annotated with variable modifications. * 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. * Fixed Modifications: The fixed modifications. * Spectrum File: The spectrum file. * Spectrum Title: The title of the spectrum. * Spectrum Scan Number: The spectrum scan number. * RT: Retention time * m/z: Measured m/z * Measured Charge: The charge as given in the spectrum file. * Identification Charge: The charge as inferred by the search engine. * Theoretical Mass: The theoretical mass of the peptide. * Isotope Number: The isotope number targetted by the instrument. * Precursor m/z Error: The precursor m/z matching error. * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs). * Confidence: Confidence in percent associated to the retained PSM. * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no). * Validation: Indicates the validation level of the protein group. ------ **Citation** To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker </help> </tool>