diff --git a/tools/peptideshaker/README.rst b/tools/peptideshaker/README.rst index d46c86279..441316e51 100644 --- a/tools/peptideshaker/README.rst +++ b/tools/peptideshaker/README.rst @@ -9,7 +9,7 @@ GalaxyP - PeptideShaker Description ----------- -Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker. +Perform protein identification combining numerous search engines and de novo sequencing algorithms (using SearchGUI) followed by peptide and protein inference with PeptideShaker. Includes tool wrappers for FastaCLI, IdentificationParametersCLI, SearchGUI and PeptideShaker. @@ -19,7 +19,7 @@ FastaCLI adds decoy sequences to any fasta file. The Identification Parameters tool allows to create a parameters (par) file which can be (re)used later to parameterize SearchGUI or PeptideShaker. -The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. +The SearchGUI tool takes any number of mgf files and performs searches or de novo sequencing on these. It creates a large zip archive with all search results, the original database when provided, and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. diff --git a/tools/peptideshaker/macros_basic.xml b/tools/peptideshaker/macros_basic.xml index f3f58e8df..b9e4c00ee 100755 --- a/tools/peptideshaker/macros_basic.xml +++ b/tools/peptideshaker/macros_basic.xml @@ -12,10 +12,10 @@ 24.2 4 - 4.0.41 - 2 - 2.0.33 - 2 + 4.3.17 + 0 + 3.0.13 + 0 10.1186/1471-2105-12-70 diff --git a/tools/peptideshaker/peptide_shaker.xml b/tools/peptideshaker/peptide_shaker.xml index 99a1db43f..6a775b6cc 100755 --- a/tools/peptideshaker/peptide_shaker.xml +++ b/tools/peptideshaker/peptide_shaker.xml @@ -728,7 +728,7 @@ **What it does** -PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. +PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines and de novo sequencing algorithms, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda, Novor, DirecTag, InstaNovo, InstaNovo+ and mzIdentML. http://compomics.github.io/projects/peptide-shaker.html diff --git a/tools/peptideshaker/searchgui.xml b/tools/peptideshaker/searchgui.xml index 13aed05c3..020582aa3 100755 --- a/tools/peptideshaker/searchgui.xml +++ b/tools/peptideshaker/searchgui.xml @@ -11,6 +11,7 @@ searchgui + instanovo zip @@ -33,7 +34,9 @@ ## echo the search engines to run (single quotes important because X!Tandem) echo '$search_engines_options.engines'; - echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}'; + #if $input_fasta_file: + echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}'; + #end if ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties; @@ -53,8 +56,10 @@ ## copy the input .par file to the working folder cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par'; - ## copy the input .fasta file to the working folder - cp '${input_fasta_file}' './input_fasta_file.fasta'; + #if $input_fasta_file: + ## copy the input .fasta file to the working folder + cp '${input_fasta_file}' './input_fasta_file.fasta'; + #end if ################ @@ -65,7 +70,9 @@ --exec_dir="\$cwd/${bin_dir}" -use_log_folder 1 -spectrum_files \$cwd - -fasta_file "\$cwd/input_fasta_file.fasta" + #if $input_fasta_file: + -fasta_file "\$cwd/input_fasta_file.fasta" + #end if -output_folder \$cwd/output -id_params ./SEARCHGUI_IdentificationParameters.par -temp_folder \$cwd/temp_folder @@ -147,6 +154,24 @@ -directag 0 #end if + #if 'InstaNovo' in $engines_list: + -instanovo 1 + #else + -instanovo 0 + #end if + + #if 'InstaNovoPlus' in $engines_list: + -instanovo_plus 1 + #else + -instanovo_plus 0 + #end if + + #if 'InstaNovoRefine' in $engines_list: + -instanovo_refine 1 + #else + -instanovo_refine 0 + #end if + ## single zip file -output_option 0 @@ -169,7 +194,7 @@ - + - + Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X (use SG 4.0.22 to solve any problem running MsAmanda). - MetaMorpheus only produce results when using mzML format. + MetaMorpheus only produce results when using mzML format. InstaNovo with refinement first predicts with InstaNovo and then refines those predictions with InstaNovo+. @@ -197,6 +222,9 @@ --> + + + @@ -353,10 +381,12 @@ Runs multiple search engines on any number of MGF peak lists using SearchGUI. Default: X! Tandem and MS-GF+ are executed. -Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed. +Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag, Novor, InstaNovo, InstaNovo+ and InstaNovo with refinement can be executed. **Input FASTA** +The FASTA input is required when running database search engines. It can be omitted for de novo-only runs such as InstaNovo, InstaNovo+ or InstaNovo with refinement. + In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences) and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format: