# HG changeset patch # User bgruening # Date 1398980476 14400 # Node ID 149d652fc9f5ce4ca524011ba6a778f21ca3656c # Parent d833f714faa69300336c2045d70cdeb39c75f452 Uploaded diff -r d833f714faa6 -r 149d652fc9f5 dbtoolkit-4.2/LICENSE-2.0.txt --- a/dbtoolkit-4.2/LICENSE-2.0.txt Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff -r d833f714faa6 -r 149d652fc9f5 dbtoolkit-4.2/dbtoolkit-4.2.jar Binary file dbtoolkit-4.2/dbtoolkit-4.2.jar has changed diff -r d833f714faa6 -r 149d652fc9f5 dbtoolkit-4.2/lib/jargs-1.0.jar --- a/dbtoolkit-4.2/lib/jargs-1.0.jar Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ - - - - - - http://searchgui.googlecode.com/files/SearchGUI-1.13.1_mac_and_linux.zip - tar -xf $DIR_NAME/*.tar - cd $DIR_NAME - chmod -R $DIR_NAME/*resources - - . - $INSTALL_DIR/ - - mkdir -p $BIN_DIR - - $INSTALL_DIR - - - - - This package downloads and installs the SearchGUI scripts develped as part of the Peptideshaker tool. - (https://github.com/jmchilton/peptide-shaker). - - - - - - - - http://peptide-shaker.googlecode.com/files/PeptideShaker-0.20.1.zip - chmod -R o+w resources - - . - $INSTALL_DIR/ - - mkdir -p $BIN_DIR - - $INSTALL_DIR - - - - - This package downloads and installs the peptideshaker tool as a part of the peptideshaker framework. - (https://github.com/jmchilton/peptide-shaker). - - - - diff -r d833f714faa6 -r 149d652fc9f5 dbtoolkit-4.2/lib/log4j-1.2.12.jar Binary file dbtoolkit-4.2/lib/log4j-1.2.12.jar has changed diff -r d833f714faa6 -r 149d652fc9f5 dbtoolkit-4.2/lib/utilities-3.8.7.jar Binary file dbtoolkit-4.2/lib/utilities-3.8.7.jar has changed diff -r d833f714faa6 -r 149d652fc9f5 peptide_shaker.xml --- a/peptide_shaker.xml Sat Apr 12 11:50:34 2014 -0400 +++ b/peptide_shaker.xml Thu May 01 17:41:16 2014 -0400 @@ -3,6 +3,7 @@ peptide_shaker searchgui + Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. @@ -19,12 +20,25 @@ #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s '$mgf' 'spectra/$input_name'; #end for + ln -s $input_database input_database.fasta; - java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI - ##SearchCLI - -spectrum_files \$cwd/spectra - -output_folder \$cwd/output - -ppm $precursor_ion_tol_units + ########################################### + #### 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 input_database_decoy.fasta -temp_folder `pwd`; + ln -sf input_database_decoy.fasta input_database.fasta; + #end if + + ##################################################### + ## generate IdentificationParameters for SearchGUI ## + ##################################################### + + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI + -temp_folder `pwd` + -out SEARCHGUI_IdentificationParameters.parameters + -prec_ppm $precursor_ion_tol_units -prec_tol $precursor_ion_tol -frag_tol $fragment_tol -enzyme '$enzyme' @@ -36,61 +50,157 @@ #if $variable_mods_str -variable_mods "$variable_mods_str" #end if + -min_charge $min_charge + -max_charge $max_charge -mc $missed_cleavages - #if $advanced.specify: - -xtandem $advanced.xtandem - #if $advanced.omssa.run_omssa - #set $omssa = 1 + -fi $forward_ion + -ri $reverse_ion + -db input_database.fasta + + #if $advanced.advanced_type_selector == "advanced": + + ##if $advanced.xtandem.xtandem_selector == "yes" + ##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" + ##end if + + ##if $advanced.ms_amanda.ms_amanda_selector == "yes" + ##end if + + #end if + ; + + ################ + ## Search CLI ## + ################ + java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI + -temp_folder `pwd` + -spectrum_files \$cwd/spectra + -output_folder \$cwd/output + -id_params SEARCHGUI_IdentificationParameters.parameters + + -threads "\${GALAXY_SLOTS:-12}" + -correct_titles $correct_titles + -mgf_splitting $mgf_splitting + -mgf_spectrum_count $mgf_spectrum_count + + #if $advanced.advanced_type_selector == "advanced": + + #if $advanced.xtandem.xtandem_selector == "yes" + -xtandem 1 #else - #set $omssa = 0 + -xtandem 0 #end if - -omssa $omssa - #if $omssa == 1 - -hitlist_length ${advanced.omssa.hitlist_length} - -remove_prec ${advanced.omssa.remove_precursor} - -scale_prec ${advanced.omssa.scale_precursor} - -estimate_charge ${advanced.omssa.estimate_charge} + #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 + #end if - -db $input_database; + ; + ######################################################### + ## generate IdentificationParameters for PeptideShaker ## + ######################################################### + java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI + -temp_folder `pwd` + -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 $reverse_ion + -db input_database.fasta + ; + ###################### + ## PeptideShakerCLI ## + ###################### java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI - ##PeptideShakerCLI + -temp_folder `pwd` -experiment '$exp_str' -sample '$samp_str' -replicate 1 -spectrum_files \$cwd/spectra -identification_files \$cwd/output - -search_params \$cwd/output/SearchGUI.parameters - -out_txt_1 \$cwd/output_reports - #if $processing_options.specify + -out \$cwd/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} - -psm_FLR ${processing_options.psm_flr} - #if str($processing_options.a_score.use) == "1" - #set $a_score = 1 - #else - #set $a_score = 0 + -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 - -a_score $a_score - #if str($a_score) == "1" - -a_score_neutral_losses ${processing_options.a_score.neutral_losses} - #end if + -protein_fraction_mw_confidence $processing_options.protein_fraction_mw_confidence #end if - #if $filtering_options.specify + + + ##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 - -out \$cwd/output.cps ; + + ##Optional output parameters: + ##Output folder for text summary - format 1 (three files: proteins, peptides and psms, soon deprecated). + -out_txt_1 \$cwd/output_reports + + ; + cp -R ./* /home/bag/test/foo; mv output_reports/*peptides.txt peptides.txt ; mv output_reports/*psms.txt psms.txt ; mv output_reports/*proteins.txt proteins.txt @@ -101,6 +211,9 @@ + + + Lys-N (K) - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + z - - - + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + - - - + + + + + + - + + - - - + + + + + + @@ -220,8 +613,9 @@ - - + + + diff -r d833f714faa6 -r 149d652fc9f5 reverse.py --- a/reverse.py Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -#!/usr/bin/env python -from os.path import join -import sys -from optparse import OptionParser -from ConfigParser import SafeConfigParser -import subprocess - -DEBUG = False - -def main(): - (options, args) = _parse_args() - _run_shell("cat '%s' > '%s'" % (options.input, options.output)) - _run_dbtoolkit("com.compomics.dbtoolkit.toolkit.ReverseFASTADB", "'%s' | head --lines -4 >> '%s'" % (options.input, options.output), options) - - -def _run_shell(command): - if DEBUG: - print "Running shell command %s" % command - _exec(command) - - -def _run_dbtoolkit(java_class, command, args): - command_prefix = "java -cp %s" % _dbtoolkit_jar_path( args.script_path ) - _exec("%s %s %s" % (command_prefix, java_class, command)) - - -def _dbtoolkit_jar_path( script_path ): - jar_path = join(script_path, "dbtoolkit-4.2", "dbtoolkit-4.2.jar") - return jar_path - -def _exec(command): - proc = subprocess.Popen(args=command, shell=True) - return_code = proc.wait() - if return_code != 0: - print "Error executing command [%s], return code is %d" % (command, return_code) - sys.exit(return_code) - - -def _parse_args(): - parser = OptionParser() - parser.add_option("-i", "--input") - parser.add_option("-o", "--output") - parser.add_option("-s", "--script_path") - return parser.parse_args() - - -if __name__ == "__main__": - main() diff -r d833f714faa6 -r 149d652fc9f5 reverse.xml --- a/reverse.xml Sat Apr 12 11:50:34 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - Creates a target-decoy database for use with Peptide Shaker - - PEPTIDESHAKER_SCRIPT_PATH - - - reverse.py - --input='$input' - --output='$output' - --script_path \$PEPTIDESHAKER_SCRIPT_PATH - - - - - - - - -**What it does** - -Given an input database, this tool will produce a target-decoy -database in the format required by PeptideShaker using dbtoolkit. - ------- - -**Citation** - -For the underlying tool, please cite `Martens et al. DBToolkit: processing protein databases for peptide-centric proteomics. Bioinformatics (2005) vol. 21 (17) pp. 3584-5`. - -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/peptideshaker . - - - diff -r d833f714faa6 -r 149d652fc9f5 tool_dependencies.xml --- a/tool_dependencies.xml Sat Apr 12 11:50:34 2014 -0400 +++ b/tool_dependencies.xml Thu May 01 17:41:16 2014 -0400 @@ -4,9 +4,12 @@ $REPOSITORY_INSTALL_DIR - + - + +