Mercurial > repos > bgruening > peptideshaker
changeset 33:068abf6b3ea0 draft
Uploaded
| author | iracooke |
|---|---|
| date | Mon, 15 Dec 2014 21:00:40 -0500 |
| parents | 1767cecc8635 |
| children | 60fea12cce9a |
| files | searchgui.xml |
| diffstat | 1 files changed, 343 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/searchgui.xml Mon Dec 15 21:00:40 2014 -0500 @@ -0,0 +1,343 @@ +<tool id="search_gui" name="Search GUI" version="1.23.0"> + <description> + Perform protein identification using various search engines and prepare results for input to Peptide Shaker + </description> + <requirements> + <requirement type="package" version="1.23">searchgui</requirement> + </requirements> + + <expand macro="stdio" /> + <command> +<![CDATA[ + #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 + + @GENERAL_PARAMETERS@ + + -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 + + #if $advanced.myrimatch.myrimatch_selector == "yes" + -myrimatch 1 + #else + -myrimatch 0 + #end if + + #if $advanced.comet.comet_selector == "yes" + -comet 1 + #else + -comet 0 + #end if + + #else + -ms_amanda 0 + #end if + + ## single zip file + -output_option 0 + + 2>> $temp_stderr) + + && + + 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" type="boolean" truevalue="True" falsevalue="False" checked="true" + label="Create a concatenated target/decoy database before running PeptideShaker" + 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" /> + + <expand macro="general_options"/> + + <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" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" + label="Add missing spectrum titles" 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="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" type="integer" value="15" + label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> + <param name="xtandem_min_frag_mz" type="integer" value="200" + label="X!Tandem: Min Frag m/z" 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" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> + <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> + <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" + label="X!Tandem: Spectrum synthesis, refinement" 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" type="boolean" truevalue="1" falsevalue="0" + label="Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> + <param name="msgf_min_pep_length" type="integer" value="6" + label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" type="integer" value="30" + label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" type="select" format="text" + label="Number of tolerable termini" 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> + + <conditional name="myrimatch"> + <param name="myrimatch_selector" type="select" label="Run MyriMatch search"> + <option value="yes">Search with MyriMatch</option> + <option value="no" selected="True">No MyriMatch search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + <conditional name="comet"> + <param name="comet_selector" type="select" label="Run Comet search"> + <option value="yes">Search with Comet</option> + <option value="no" selected="True">No Comet search</option> + </param> + <when value="no" /> + <when value="yes"> + </when> + </conditional> + + </when> + </conditional> + + </inputs> + <outputs> + <data format="bgzip" name="searchgui_results" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + </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="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. + + + </help> + <expand macro="citations" /> +</tool>