Mercurial > repos > galaxyp > peptideshaker
changeset 18:a5f9b959d5d1 draft
Uploaded
| author | iracooke |
|---|---|
| date | Wed, 25 Jun 2014 11:49:45 -0400 |
| parents | 6cdbfdffb38e |
| children | 7e61179c5952 |
| files | COPYING README.md peptide_shaker.xml repository_dependencies.xml searchgui_mods.loc.sample test-data/._tinyoutput.cps test-data/tinydb.fasta test-data/tinyoutput.cps test-data/tinyspectra.mgf tool_dependencies.xml |
| diffstat | 10 files changed, 1258 insertions(+), 6298 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Jun 25 11:49:45 2014 -0400 @@ -0,0 +1,74 @@ +GalaxyP - PeptideShaker +======================= + +* Home: <https://bitbucket.org/galaxyp/peptideshaker> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> +* Tool ID: `peptideshaker` +* Tool Type: `default` + + +Description +----------- + +Perform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. + +Tool wrapper for SearchGUI and PeptideShaker. This tool takes any number of mgf files and performs X! Tandem and OMSSA searches on these via SearchGUI and merges the results using PeptideShaker. + +Configuration +------------- + +This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell; + +export _JAVA_OPTIONS='-Xmx1500M' + +It is also possible to set this on a per tool basis using advanced features of the galaxy job config system + +Note: + +- SearchGUI requires a version greater than 1.12.2 which contained several bugs preventing this from working on the command-line and via Linux. + +- PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. + +See: + +* <https://code.google.com/p/peptide-shaker/> +* <https://code.google.com/p/searchgui/> + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. + + +Authors +------- + +Authors and contributors: + +* Bjoern Gruening <bjoern.gruening@gmail.com> +* Ira Cooke +* Cody Wang +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_shaker.xml Wed Jun 25 11:49:45 2014 -0400 @@ -0,0 +1,958 @@ +<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Jun 25 11:49:45 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui_mods.loc.sample Wed Jun 25 11:49:45 2014 -0400 @@ -0,0 +1,210 @@ +methylation of k +oxidation of m +carboxymethyl c +carbamidomethyl c +deamidation of n and q +propionamide c +phosphorylation of s +phosphorylation of t +phosphorylation of y +m cleavage from protein n-term +acetylation of protein n-term +methylation of protein n-term +tri-methylation of protein n-term +beta methythiolation of d +methylation of q +tri-methylation of k +methylation of d +methylation of e +methylation of peptide c-term +tri-deuteromethylation of d +tri-deuteromethylation of e +tri-deuteromethylation of peptide c-term +n-formyl met addition +2-amino-3-oxo-butanoic acid t +acetylation of k +amidation of peptide c-term +beta-methylthiolation of d (duplicate of 13) +carboxyamidomethylation of k +carboxyamidomethylation of h +carboxyamidomethylation of d +carboxyamidomethylation of e +carbamylation of k +carbamylation of n-term peptide +citrullination of r +oxidation of c to cysteic acid +di-iodination of y +di-methylation of k +di-methylation of r +di-methylation of peptide n-term +oxidation of f to dihydroxyphenylalanine +gammathiopropionylation of k +gammathiopropionylation of peptide n-term +farnesylation of c +formylation of k +formylation of peptide n-term +oxidation of w to formylkynurenin +fluorophenylalanine +beta-carboxylation of d +gamma-carboxylation of e +geranyl-geranyl +glucuronylation of protein n-term +glutathione disulfide +ubiquitinylation residue +guanidination of k +oxidation of h to n +oxidation of h to d +homoserine +homoserine lactone +oxidation of w to hydroxykynurenin +hydroxylation of d +hydroxylation of k +hydroxylation of n +hydroxylation of p +hydroxylation of f +hydroxylation of y +iodination of y +oxidation of w to kynurenin +lipoyl k +methyl ester of peptide c-term (duplicate of 18) +methyl ester of d +methyl ester of e (duplicate of 17) +methyl ester of s +methyl ester of y +methyl c +methyl h +methyl n +methylation of peptide n-term +methyl r +myristoleylation of g +myristoyl-4h of g +myristoylation of peptide n-term g +myristoylation of k +formylation of protein n-term +nem c +nipcam +oxidation of w to nitro +oxidation of y to nitro +o18 on peptide n-term +di-o18 on peptide n-term +oxidation of h +oxidation of w +phosphopantetheine s +palmitoylation of c +palmitoylation of k +palmitoylation of s +palmitoylation of t +phosphorylation of s with prompt loss +phosphorylation of t with prompt loss +phosphorylation with prompt loss on y +phosphorylation with neutral loss on c +phosphorylation with neutral loss on d +phosphorylation with neutral loss on h +propionyl light k +propionyl light on peptide n-term +propionyl heavy k +propionyl heavy peptide n-term +pyridyl k +pyridyl peptide n-term +pyro-cmc +pyro-glu from n-term e +pyro-glu from n-term q +oxidation of p to pyroglutamic acid +s-pyridylethylation of c +semet +sulfation of y +sulphone of m +tri-iodination of y +tri-methylation of r +n-acyl diglyceride cysteine +icat light +icat heavy +camthiopropanoyl k +phosphorylation with neutral loss on s +phosphorylation with neutral loss on t +phosphorylation of s with etd loss +phosphorylation of t with etd loss +heavy arginine-13c6 +heavy arginine-13c6-15n4 +heavy lysine-13c6 +pngasf in o18 water +beta elimination of s +beta elimination of t +oxidation of c to sulfinic acid +arginine to ornithine +dehydro of s and t +carboxykynurenin of w +sumoylation of k +itraq114 on nterm +itraq114 on k +itraq114 on y +itraq115 on nterm +itraq115 on k +itraq115 on y +itraq116 on nterm +itraq116 on k +itraq116 on y +itraq117 on nterm +itraq117 on k +itraq117 on y +mmts on c +heavy lysine - 2h4 +heavy lysine - 13c6 15n2 +asparagine hexnac +asparagine dhexhexnac +serine hexnac +threonine hexnac +palmitoleyl of s +palmitoleyl of c +palmitoleyl of t +chd2-di-methylation of k +chd2-di-methylation of peptide n-term +maleimide-peo2-biotin of c +phosphorylation of h +oxidation of c +oxidation of y (duplicate of 64) +uniblue a on k +deamidation of n +trideuteration of l (silac) +tmt duplex on k +tmt duplex on n-term peptide +tmt 6-plex on k +tmt 6-plex on n-term peptide +itraq8plex:13c(7)15n(1) on nterm +itraq8plex:13c(7)15n(1) on k +itraq8plex:13c(7)15n(1) on y +itraq8plex:13c(6)15n(2) on nterm +itraq8plex:13c(6)15n(2) on k +itraq8plex:13c(6)15n(2) on y +selenocysteine +carboxymethylated selenocysteine +dimethyl 2d n-terminus +dimethyl 2d k +gtp desthiobiotinc12 +gtp desthiobiotinc13 +user modification 5 +user modification 6 +user modification 7 +user modification 8 +user modification 9 +user modification 10 +user modification 11 +user modification 12 +user modification 13 +user modification 14 +user modification 15 +user modification 16 +user modification 17 +user modification 18 +user modification 19 +user modification 20 +user modification 21 +user modification 22 +user modification 23 +user modification 24 +user modification 25 +user modification 26 +user modification 27 +user modification 28 +user modification 29 +user modification 30
--- a/test-data/tinydb.fasta Wed Jun 25 11:49:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ ->cds.comp107265_c0_seq1|m.36816 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.94 EValue:9.0e-68 -LKSSFESSFSIKSRDVTFGNSMNITMVPPELEFFKDNRHKEKSEMQDLNTRLESYLSVGKDDSDANLKLMQELEEIKNGIKTETNNIKATFEAELGQLKNLLDDIDHDKNQVIVIGDNNDEMYKDLEQRIKNYNDMEMIHLSKIRQLDNLLSNYGLKMNQLQKKIGFLCEEKDRDIESINKLRADIDVAKNDLSNEILLRTDAQNRCQSLEEDIEFTKEVHQRELSNMIALADYDPVSQSMDWWNDEFARCIKEIQDEYEDRLNNIQYDMDSHYNSKIQDVETTILQSSAKSEMLDQCSMLENSNAEIEDQTSELEKKNAMLKEQNDLLNRGIREIQSQFETLITEKQSEMLEIRKHFEQSLADLQAIVDDNLSLQMEIMSYKKLLECEELRVGIYPESNANENQGDQGQRQNEQITEPITETIPKRKKPERKISYQRSSKGPLTISECKSDGSYILIENMDQYDGQNLGGWRLVQNVDGMEEYDYTFSRYYLGPGESVKIWAENAGPKGVNDLVWDDLKCLGIGEKVITSLMNQKGKEKSSYTQKAIYKV ->cds.comp307584_c0_seq2|m.40556 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 39.47 EValue:1.0e-14 -DDNYDSLQYSFPKSDHQRKTTYQRSAKGPITITRVQPDGSYIEIENTNIAVNEDISGWKMVQCTDDKIYEYIFDDHVLNGGTCVKIWANGLSGKEENDLVWIDRTCLTTGSVVTTTLMDYNGNEKATFTQ ->cds.comp376950_c0_seq1|m.42080 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 41.38 EValue:1.0e-32 -KELEDINEDNLGRLRRQDEDVSNYEAQNASLRRKCDNLQADKDRDRNNVEKLKGEVTSLRNDLMMETVSRIDSQNKCQTLREELEFLKDIHSQELKELSPTLGKDPFAKSKEWWSSEFSNCIREIQEEYDNRLDSIKTDMDNYYTLKVQEIQTGAAR ->cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67 -METTKERKEKSTVVTKRQSMGATAHVQPKFIQVNRRSHVVGAGLGGGSMGSMNQSMSLHGGRASLGMAAGVAGGIATKDMGTMKVKREGEKKDMQNLNDRFAGYIAKVRSLQAENEQLRLKLSKKRREFDVEPLKEAYQAEIDEAKNLLLDANKENGELKISITTYEEEIEDLHATARINEDRIDELQDKVNKLIDENSHREAECSMLHKKLDELEKQVAHWRAKYNEVNTQLQATRADLKDETQQRIFLQQKVGNLEEELEFLRSVTDAEIKEYKAMLSKEDDTGTNVSAAWNNEMSNCMKELREEYDQRLADISDEMSARYESQLSQIRQSAHAEPVAAVHTKSEKSTGMVSVQKDMRIKELESQLERMKMEIITITNQLQRSNEDLENEKDLRTTEVNKLHVEMESMIEELQMLMDAKLSLELEIAAYRKLLEGEENRISTGYITENIGGFRSEAGDNLANILEFGSGGGGGGGGGGSGSGSGSGLAGDSGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10 -SGLAGDSDTMRASTSTLTGRLTIQRSSKSVISIGEVESEGQYVTLENTSSGRSKTSVNMKGWKLDRLISATSISPEHKIDFLFKDPVVLEGEQSIKIWAKNYQKMAKKGDIIATVDEWGPVNRNSVFSLYDEKDALKANLSTKVVT ->cds.comp41890_c0_seq1|m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20 -YQSPTPALVKGELQEHSTYRKNNKGPVAISETDRDGSFILLENTSNSHTVDLSGWKIMQNSDNIDISEYEIENLVLKPGGFAKVWANGMGDPNSGDLVWHNKSRLGVGAKVNTVLLNTRGDEKATYNLETTYNL ->cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGTTSITTGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92 -MEKQGVETRQTVTTSRQSVNYKPFTQSKNIVINRVSLSPGTAMSTMQRSRSSMSSGLGLGGHLQAGVLGNISHKGVASMKLKREGEKKELQDLNERLANFIEQARFLEAENKALRDALNKSKKDFDPEPLKQMYQIEINEAKKLLDDANNDNGNLKVRINTLEDELEDLRAQLRHSNDVNDQLQNNIDTLNDDIARRIADNEMLKRKVQELEKQLADWKAKYAHVDTQLQGLRIDLQEETCQRLAESTRAQALEEELNFLRSVTDAEIKEYKAMLMKEDNVPQMREYWNNELSKCMREIRDEYDNQLNLLSADLESKYQVQLNEIRLGATKGNAESAQASEENRRLRSQITDKDSHMMDLQSQIDKLKSQVHLLTSELDSTTAELDNEKTLRVSEVQKLNTELEGVIKELQLLMDAKLSLELEIAAYRKLLEVEENRLSIGSMTQMVGGYRGQTEDALANILERSGASFEASSSMGESGRVTMQRSSKGVISIAEVDNTGRYVTLDNTSTTRMKRLQNLKGWKIKREFIRTNSLQELSFEYIINRDTSLDAQQNIRVWAKNFEKDPEIKPDDIISSVADWGQVNRNSIITLYDENGVEKATLTIKVVF ->cds.comp55448_c0_seq1|m.24261 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 96.04 EValue:0.0 -MRRIKKKITLDVRVTELIDQLERQQKELEESRTYHQIDQEQIARQNQQLADLEGEISMLRRSIESLEKEKMRQSNILAKMNDELEKLRMDLNNETINHLDAENRRQTLEEELEFQKDVHAQELKELAALAYRDTTAENREFWRNELAQAIRDIQQEYDAKCDQMRGDIEAYYNLKVQEFRTGATKQNMEVTRNKEENTKLRSNMNEVRNRLADLEARNAQLERTNQDLLRDLEEKDRQNELESCQYKEEITKLRGEMESILKELQDLMDIKLSLELEIAAYRKLLEGEESRVGMKQIVEQVVGARPNEAEVLSSILTRSEGGYEATGDSQISMKMMRGELAAKTTYQRTSKGPVSIKEADSQGQFIALETKKEENITGWKIVRKVDDNMVYSYEIPNVVLKTGTVIKIWSKSHQAQARGDDIVSRENDTWGTGSNVVTILQNEKGEEKANYTQNTVYQ ->cds.comp55448_c0_seq1|m.24262 RecName: Full=60 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 91.49 EValue:5.0e-87 -MSGGFSYSAKIHPRTGYVSRTSQSPYRSSMGSNAAFTRSYEFNYGATAMPGAYANISSTGVNHVKANREREKQDMRDLNERFANYIEKVRFLEAQNKKLAGELEELKSKWGKETSAIKEMYETELEEARKLIDATNKEKNYLGRESN ->cds.comp8310_c0_seq2|m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16 -FKDTCIRDKTDMKGLNERLSEFIEVARYNAILAKKLEKTIKRFHSQEIPEDVERIYEATIKKLRKLLVVFENERDNERAKNLKLQTECAKLKESLEDLKAKEIENRDRLISKFKILEDLQSKAIRIEKNIEIVAEENVLKNNKIEKLKKHFENLKSKITSERRNRSTHKESYDEVKEDFGIFKELKNQQLSSVRFPKYKDSIKYLRKQWSNEFSKCIKELQNEYESRVSSVKEELESNYCTKTEEIQNYVLKSNYESDFLKNRNLVAEESMNMLKNKFKEAKKENVLLNHEKEELEIEFNKSKNEYDHLAEEKNNEILNFKEYAEKILIQLTEILEINNHLQFEIEYYKTVITSGETKIDFDFDGLDDECMTSINSELP
--- a/test-data/tinyspectra.mgf Wed Jun 25 11:49:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6153 +0,0 @@ -BEGIN IONS -TITLE= Cmpd 636, +MSn(730.3981), 66.9 min -PEPMASS=730.39814 92569 -CHARGE=2+ -156.06738 122 -175.10440 1049 -186.08322 120 -187.12501 241 -188.06515 494 1+ -193.09503 180 -197.12522 208 -199.17309 1374 1+ -204.08687 454 1+ -213.14347 128 -215.11998 747 1+ -227.17167 1524 1+ -229.12416 156 -233.09327 3574 1+ -236.99586 113 -243.14264 571 1+ -244.07481 236 -245.12901 240 -246.12647 275 -256.20038 432 1+ -258.12496 133 -260.19976 423 -261.09190 17853 1+ -270.16206 114 -274.12614 207 -283.15366 136 -284.18559 406 1+ -286.14626 237 -287.10013 105 -301.15759 131 -303.17924 2962 1+ -310.21264 944 1+ -315.13250 122 -316.16696 108 -326.16601 145 -328.21268 874 1+ -335.13393 406 1+ -338.20704 186 -339.16449 110 -342.17857 106 -344.13585 148 -346.17426 809 1+ -356.21762 685 1+ -358.15839 265 -359.26213 106 -362.14671 528 1+ -366.16564 103 -370.14930 136 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 25 11:49:45 2014 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="searchgui" version="1.19.5"> + <repository changeset_revision="e544ffa7ea6f" name="package_searchgui_1_19" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="peptide_shaker" version="0.31.4"> + <repository changeset_revision="45ee9e65471f" name="package_peptideshaker_0_31" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <!--<package name="blast+" version="2.2.29"> + <repository name="package_blast_plus_2_2_29" owner="iuc" /> + </package>--> +</tool_dependency>