comparison searchgui.xml @ 59:943a34df6047 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"

58:07ff622ec007

        ## Search CLI ##
        ################
        echo 'running search gui' &&
        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
            --exec_dir="\$cwd/${bin_dir}"
            -spectrum_files \$cwd
            -fasta_file "\$cwd/input_fasta_file.fasta"
            -output_folder \$cwd/output
            -id_params ./SEARCHGUI_IdentificationParameters.par
            -temp_folder \$cwd/temp_folder

        <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 name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
            help="Select appropriate MGF/MZML dataset(s) from history" />

        <!-- 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">
                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers.</help>
                <option value="X!Tandem" selected="True">X!Tandem</option>
                <option value="MSGF" selected="True">MS-GF+</option>
                <option value="OMSSA">OMSSA</option>
                <option value="Comet">Comet</option>
                <option value="Tide">Tide</option>
                <option value="MyriMatch">MyriMatch</option>
                <option value="MS_Amanda">MS_Amanda</option>
                <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
                <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
                <!-- Windows only
                <option value="Andromeda">Andromeda</option>
                -->
                <!-- New with version 3.0
                -->

            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
            <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
            <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
        </test>

        <!-- Test that search works with MSAmanda with default parameters works-->
        <test>
            <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>

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, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.

**Input FASTA**

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:

59:943a34df6047

        ## Search CLI ##
        ################
        echo 'running search gui' &&
        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
            --exec_dir="\$cwd/${bin_dir}"
            -use_log_folder 0
            -spectrum_files \$cwd
            -fasta_file "\$cwd/input_fasta_file.fasta"
            -output_folder \$cwd/output
            -id_params ./SEARCHGUI_IdentificationParameters.par
            -temp_folder \$cwd/temp_folder

        <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 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">
                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. 
                    MetaMorpheus only produce results when using mzML format.</help>
                <option value="X!Tandem" selected="True">X!Tandem</option>
                <option value="MSGF" selected="True">MS-GF+</option>
                <option value="OMSSA">OMSSA</option>
                <option value="Comet">Comet</option>
                <option value="Tide">Tide</option>
                <option value="MyriMatch">MyriMatch</option>
                <option value="MS_Amanda">MS_Amanda</option>
                <option value="MetaMorpheus">MetaMorpheus</option>
                <!-- Windows only
                <option value="Andromeda">Andromeda</option>
                -->
                <!-- New with version 3.0
                -->

            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
            <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
            <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
            <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
        </test>
        
        
        <!-- Test that search works with MetaMorpheus with default parameters works-->
        <!-- Test data has been taken from metamorpheus galaxy tool -->
        <test>
            <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
            <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" />
            <param name="engines" value="MetaMorpheus"/>
            <output name="searchgui_results" ftype="searchgui_archive">
                <assert_contents>
                    <has_size value="798597" delta="10000"/>
                </assert_contents>
            </output>
        </test>

        <!-- Test that search works with MSAmanda with default parameters works-->
        <test>
            <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>

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.

**Input FASTA**

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: