Skip to content

Bump PeptideShaker wrappers for InstaNovo support #828

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
BioGeek wants to merge 1 commit into
base: master
Choose a base branch
from
Draft

Bump PeptideShaker wrappers for InstaNovo support #828

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions tools/peptideshaker/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand All @@ -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.

Expand Down
8 changes: 4 additions & 4 deletions tools/peptideshaker/macros_basic.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@
</xml>
<token name="@PROFILE@">24.2</token>
<token name="@SEARCHGUI_MAJOR_VERSION@">4</token>
<token name="@SEARCHGUI_VERSION@">4.0.41</token>
<token name="@SEARCHGUI_VERSION_SUFFIX@">2</token>
<token name="@PEPTIDESHAKER_VERSION@">2.0.33</token>
<token name="@PEPTIDESHAKER_VERSION_SUFFIX@">2</token>
<token name="@SEARCHGUI_VERSION@">4.3.17</token>
<token name="@SEARCHGUI_VERSION_SUFFIX@">0</token>
<token name="@PEPTIDESHAKER_VERSION@">3.0.13</token>
<token name="@PEPTIDESHAKER_VERSION_SUFFIX@">0</token>
<xml name="citations">
<citations>
<citation type="doi">10.1186/1471-2105-12-70</citation>
Expand Down
2 changes: 1 addition & 1 deletion tools/peptideshaker/peptide_shaker.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -728,7 +728,7 @@
<help>
**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

Expand Down
46 changes: 38 additions & 8 deletions tools/peptideshaker/searchgui.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
</macros>
<requirements>
<requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
<requirement type="package" version="1.2.2">instanovo</requirement>
<requirement type="package" version="3.0">zip</requirement>
</requirements>
<expand macro="stdio" />
Expand All @@ -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;
Expand All @@ -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


################
Expand All @@ -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
Expand Down Expand Up @@ -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

Expand All @@ -169,17 +194,17 @@
<inputs>
<param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>

<param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
<param format="fasta" name="input_fasta_file" type="data" optional="true" label="Fasta file" help="Required for database search engines. Optional for de novo-only runs. For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>

<param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
help="Select appropriate MGF/MZML dataset(s) from history.
Remember to choose only .mzML files when using MetaMorpheus." />

<!-- Search Engine Selection -->
<section name="search_engines_options" expanded="true" title="Search Engine Options">
<param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
<param name="engines" type="select" display="checkboxes" multiple="True" label="Search engines and de novo algorithms">
<help>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.</help>
MetaMorpheus only produce results when using mzML format. InstaNovo with refinement first predicts with InstaNovo and then refines those predictions with InstaNovo+.</help>
<option value="X!Tandem" selected="True">X!Tandem</option>
<option value="MSGF" selected="True">MS-GF+</option>
<option value="OMSSA">OMSSA</option>
Expand All @@ -197,6 +222,9 @@
-->
<option value="DirecTag">DirecTag</option>
<option value="Novor">Novor (Select for non-commercial use only)</option>
<option value="InstaNovo">InstaNovo</option>
<option value="InstaNovoPlus">InstaNovo+</option>
<option value="InstaNovoRefine">InstaNovo with refinement</option>
<validator type="no_options" message="Please select at least one output file" />
</param>
</section>
Expand Down Expand Up @@ -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:

Expand Down
Loading