Mercurial > repos > jjohnson > peptideshaker
diff searchgui.xml @ 2:eea7e945f479 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
| author | jjohnson |
|---|---|
| date | Thu, 12 Jul 2018 08:42:58 -0400 |
| parents | fa76abf69433 |
| children |
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--- a/searchgui.xml Fri Jun 08 15:58:53 2018 -0400 +++ b/searchgui.xml Thu Jul 12 08:42:58 2018 -0400 @@ -3,7 +3,7 @@ Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> <macros> - <import>macros_basic.xml</import> + <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> @@ -13,8 +13,6 @@ <command> <![CDATA[ #from datetime import datetime - #import json - #import os #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 $temp_stderr = "searchgui_stderr" @@ -26,7 +24,8 @@ export HOME=\$cwd; ## echo the search engines to run - echo '$search_engines_options.engines'; + echo "$search_engines_options.engines"; + echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; ##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; @@ -35,28 +34,291 @@ #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; #set $encoded_id = $__app__.security.encode_id($mgf.id) - echo 'Spectrums:${mgf.display_name}(API:${encoded_id}) '; + echo "Spectrums:${mgf.display_name}(API:${encoded_id}) "; #end for + ##ln -s "${input_database}" input_database.fasta; + cp "${input_database}" input_database.fasta; + + ########################################### + #### Creating decoy database #### + ########################################### + #if $protein_database_options.create_decoy: + echo "Creating decoy database."; + searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -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 + @ENZYMESCLI@ + ##################################################### + ## generate IdentificationParameters for SearchGUI ## + ##################################################### + (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + --exec_dir="\$cwd/${bin_dir}" + -out SEARCHGUI_IdentificationParameters.par + + @GENERAL_PARAMETERS@ + + -db input_database.fasta + $protein_database_options.use_gene_mapping + #if $protein_database_options.use_gene_mapping: + $protein_database_options.update_gene_mapping + #else: + -updateGeneMapping 0 + #end if + + #if $advanced_options.xtandem.xtandem_advanced == "yes" + + -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr} + -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range} + -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl} + -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro} + -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias} + -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue} + -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins} + -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences} + -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra} + ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path} + + #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes" + -xtandem_refine 1 + -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue} + + #end if + #else + -xtandem_output_spectra 1 + #end if - ## copy the input .par file to the working folder - cp '${input_zip}' './input_par_fasta.zip'; - echo '-.zip source file:'; - echo '${input_zip}'; + #if $advanced_options.omssa.omssa_advanced == "yes" + -omssa_hitlist_length ${advanced_options.omssa.hitlist_length} + -omssa_remove_prec ${advanced_options.omssa.remove_precursor} + -omssa_scale_prec ${advanced_options.omssa.scale_precursor} + -omssa_estimate_charge ${advanced_options.omssa.estimate_charge} + -omssa_memory ${advanced_options.omssa.omssa_memory} + -omssa_neutron ${advanced_options.omssa.omssa_neutron} + -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" + -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} + -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} + -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} + -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} + -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} + -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} + -omssa_methionine ${advanced_options.omssa.omssa_methionine} + -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} + -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} + -omssa_fraction ${advanced_options.omssa.omssa_fraction} + -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} + -omssa_charge ${advanced_options.omssa.omssa_charge} + -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum} + -omssa_forward ${advanced_options.omssa.omssa_forward} + -omssa_rewind ${advanced_options.omssa.omssa_rewind} + -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series} + -omssa_corr ${advanced_options.omssa.omssa_corr} + -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue} + -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length} + -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length} + -omssa_format ${advanced_options.omssa.omssa_format} + #end if + + #if $advanced_options.msgf.msgf_advanced == "yes" + -msgf_decoy ${advanced_options.msgf.msgf_decoy} + -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length} + -msgf_termini ${advanced_options.msgf.msgf_termini} + -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms} + -msgf_instrument ${advanced_options.msgf.msgf_instrument} + -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation} + -msgf_protocol ${advanced_options.msgf.msgf_protocol} + -msgf_num_matches ${advanced_options.msgf.msgf_num_matches} + -msgf_additional ${advanced_options.msgf.msgf_additional} + #end if + + #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes" + -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy} + -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}" + -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank} + -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono} + #end if + + #if $advanced_options.myrimatch.myrimatch_advanced == "yes" + -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length} + -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length} + -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass} + -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass} + -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches} + -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms} + -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation} + -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini} + -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three} + -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr} + -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff} + -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes} + -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier} + -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches} + -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak} + #end if - ## Necessary for executing tests. Specific par files need to be uncompressed to be used by the tool. - jar xvf './input_par_fasta.zip' 'Identification_Parameters_default.par' 'searchgui_tinydb1_concatenated_target_decoy.fasta'; - jar xvf './input_par_fasta.zip' Identification_Parameters_specific.par searchgui_tinydb1_concatenated_target_decoy.fasta; - if [ -f ./Identification_Parameters_default.par ];then - mv ./Identification_Parameters_default.par ./SEARCHGUI_IdentificationParameters.par; - fi; - if [ -f ./Identification_Parameters_specific.par ];then - mv './Identification_Parameters_specific.par' './SEARCHGUI_IdentificationParameters.par'; - fi; + #* Not working in tests + #if $advanced_options.andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb} + -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge} + -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il} + -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method} + -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} + #end if + *# + + #if $advanced_options.tide.tide_advanced == "yes" + #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz} + #end if + -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} + -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} + -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} + -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass} + -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} + -tide_decoy_format ${advanced_options.tide.tide_decoy_format} + -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} + -tide_print_peptides ${advanced_options.tide.tide_print_peptides} + -tide_verbosity ${advanced_options.tide.tide_verbosity} + -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} + -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term} + -tide_digestion_type ${advanced_options.tide.tide_digestion_type} + -tide_compute_sp ${advanced_options.tide.tide_compute_sp} + -tide_max_psms ${advanced_options.tide.tide_max_psms} + -tide_compute_p ${advanced_options.tide.tide_compute_p} + -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} + #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} + #end if + -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} + -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} + -tide_remove_prec ${advanced_options.tide.tide_remove_prec} + -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol} + -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator} + -tide_use_flanking ${advanced_options.tide.tide_use_flanking} + -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses} + -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} + -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} + -tide_concat ${advanced_options.tide.tide_concat} + + #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"] + #for $format in $formats: + #if str($advanced_options.tide.tide_export).strip() == $format: + -$format 1 + #else: + -$format 0 + #end if + + #end for + + -tide_remove_temp ${advanced_options.tide.tide_remove_temp} + + #end if + - ## By default we will always try to uncompress SEARCHGUI_IdentificationParameters.par and input_database.fasta - jar xvf './input_par_fasta.zip' SEARCHGUI_IdentificationParameters.par input_database.fasta; + #if $advanced_options.comet.comet_advanced == "yes" + + #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" + -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks} + -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int} + + -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec} + + + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #end if + + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #end if + + -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower} + -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper} + #end if + + #if $advanced_options.comet.comet_search.comet_search_selector == "yes" + -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type} + -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction} + -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass} + -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass} + -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches} + -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge} + -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth} + -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size} + -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms} + #end if + #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" + -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset} + -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} + #end if + #end if + + #if $advanced_options.directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff} + -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count} + -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes} + -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor} + -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment} + -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment} + -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step} + -directag_charge_states ${advanced_options.directtag.directag_charge_states} + #if str($advanced_options.directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${advanced_options.directtag.directag_output_suffix} + #end if + -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra} + -directag_deisotoping ${advanced_options.directtag.directag_deisotoping} + -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance} + -directag_tag_length ${advanced_options.directtag.directag_tag_length} + -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods} + -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count} + -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight} + -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight} + -directag_complement_weight ${advanced_options.directtag.directag_complement_weight} + #end if + + #if $advanced_options.novor.novor_advanced == "yes" + -novor_fragmentation ${advanced_options.novor.novor_fragmentation} + -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer} + #end if + + 2> $temp_stderr) + && ################ ## Search CLI ## @@ -66,15 +328,16 @@ -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output - -id_params ./SEARCHGUI_IdentificationParameters.par + @ENZYME_CONFIGUTRATION@ + -id_params SEARCHGUI_IdentificationParameters.par -threads "\${GALAXY_SLOTS:-12}" - #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' - -correct_titles "${searchgui_advanced.correct_titles}" - $searchgui_advanced.missing_titles - -mgf_splitting "${searchgui_advanced.mgf_splitting}" - -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" + #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced' + -correct_titles "${advanced_options.searchgui_advanced.correct_titles}" + $advanced_options.searchgui_advanced.missing_titles + -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}" + -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}" #end if ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created @@ -166,9 +429,20 @@ ]]> </command> <inputs> - <param format="zip" name="input_zip" type="data" label="Identification Parameters and fasta file" - help="Select a zip file with Identification Parameters (.par) and a fasta file from history"/> + <param format="fasta" name="input_database" type="data" label="Protein Database" + help="Select FASTA database from history"/> + <section name="protein_database_options" expanded="false" title="Protein Database Options"> + <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 name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" + label="gene mappings will be used and saved along with the project (UniProt databases only)" + help="This should only be enabled for UniProt databaases" /> + <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false" + label="Update gene mappings automatically from Ensembl (UniProt databases only)" + help="This should only be enabled for UniProt databaases" /> + </section> <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> @@ -177,6 +451,7 @@ <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.</help> <option value="X!Tandem" selected="True">X!Tandem</option> + <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> @@ -196,31 +471,617 @@ </param> </section> - <conditional name="searchgui_advanced"> - <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> - <option value="basic" selected="True">Default</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic" /> - <when value="advanced"> - <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> + + <!-- General Parameters --> + <expand macro="general_options"/> + + + <section name="advanced_options" expanded="false" title="Andvanced Options"> + <!-- Optional Advanced SearchGUI Parameters --> + <conditional name="searchgui_advanced"> + <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> + <option value="basic" selected="True">Default</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <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"/> + </when> + </conditional> + + <!-- X!TANDEM ADVANCED PARAMETERS --> + <conditional name="xtandem"> + <param name="xtandem_advanced" type="select" label="X!Tandem Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="xtandem_npeaks" type="integer" value="50" + label="X!Tandem: Total Peaks" 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" type="integer" value="200" + label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" + label="X!Tandem: Noise Suppression" help="Use noise suppression"/> + <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" + label="X!Tandem: Dynamic Range" value="100" type="integer" /> + <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" + label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" + label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" + label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_evalue" help="Highest value for recorded peptides" + label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> + <param name="xtandem_output_proteins" help="Controls output of protein sequences" + label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_output_sequences" help="Controls output of sequence information" + label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_output_spectra" help="Controls output of spectrum information" + label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." --> + + <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" checked="true" + label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false" + 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" checked="false" + label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true" + 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" checked="true" + label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> + <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/> + <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement" + label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> + </when> + </conditional> + </when> + </conditional> + + <!-- OMSSA ADVANCED PARAMETERS --> + <conditional name="omssa"> + <param name="omssa_advanced" type="select" label="OMSSA Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</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" /> + + <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> + <param name="omssa_neutron" type="float" value="1446.94" + label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> + <param name="omssa_low_intensity" type="float" value="0.0" + label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> + <param name="omssa_high_intensity" type="float" value="0.2" + label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> + <param name="omssa_intensity_incr" type="float" value="0.0005" + label="OMSSA: Intensity Increment" help="Intensity increment" /> + <param name="omssa_single_window_wd" type="integer" value="27" + label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" /> + <param name="omssa_double_window_wd" type="integer" value="14" + label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" /> + <param name="omssa_single_window_pk" type="integer" value="2" + label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" /> + <param name="omssa_double_window_pk" type="integer" value="2" + label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" /> + <param name="omssa_min_ann_int_pks" type="integer" value="6" + label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" /> + <param name="omssa_min_annotated_peaks" type="integer" value="2" + label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" /> + <param name="omssa_min_peaks" type="integer" value="4" + label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" /> + <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" /> + <param name="omssa_max_ladders" type="integer" value="128" + label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" /> + <param name="omssa_max_frag_charge" type="integer" value="2" + label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" /> + <param name="omssa_fraction" type="float" value="0.95" + label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" /> + <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/> + <param name="omssa_charge" type="select" + label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" > + <option value="0" >Minus</option> + <option value="1" selected="True">Plus</option> + </param> + <param name="omssa_prec_per_spectrum" type="integer" value="1" + label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> + <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> + <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> + <param name="omssa_max_frag_series" type="integer" value="100" + label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> + <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> + <param name="omssa_consecutive_p" type="float" value="0.5" + label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> + <param name="omssa_it_sequence_evalue" type="float" value="0.0" + label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> + <param name="omssa_it_spectrum_evalue" type="float" value="0.01" + label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> + <param name="omssa_it_replace_evalue" type="float" value="0.01" + label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> + <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_max_evalue" type="float" value="100" + label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" /> + <param name="omssa_it_replace_evalue" type="float" value="100" + label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" /> + <param name="omssa_hitlist_length" type="integer" value="0" + label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> + <param name="omssa_hitlist_charge" type="integer" value="30" + label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> + <param name="omssa_min_pep_length" type="integer" value="4" + label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> + <param name="omssa_max_pep_length" type="integer" value="40" + label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> + <param name="omssa_format" label="OMSSA output format" type="select" > + <option value="0" selected="True">OMX</option> + <option value="1" >CSV</option> + </param> + </when> + </conditional> + + <!-- MS-GF+ ADVANCED PARAMETERS --> + <conditional name="msgf"> + <param name="msgf_advanced" type="select" label="MSGF Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MSGF: 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="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" type="integer" value="30" + label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" type="select" format="txt" + label="MSGF: 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="MSGF: Max PTMs per peptide" type="integer" value="2"/> + + <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> + <option value="0" selected="True">Low-res LCQ/LTQ</option> + <option value="1" >High-res LTQ</option> + <option value="2" >TOF</option> + <option value="3" >Q-Exactive</option> + </param> + <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> + <option value="0" selected="True">As written in the spectrum or CID if no info</option> + <option value="1" >CID</option> + <option value="2" >ETD</option> + <option value="3" >HCD</option> + </param> + <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples"> + <option value="0" selected="True">Automatic</option> + <option value="1" >Phosphorylation</option> + <option value="2" >iTRAQ</option> + <option value="3" >iTRAQPhospho</option> + <option value="4" >TMT</option> + <option value="5" >Standard</option> + </param> + <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> + <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export"> + <option value="0" selected="True">output basic scores only</option> + <option value="1" >output additional features</option> + </param> + </when> + </conditional> + + <!-- MS-AMANDA ADVANCED PARAMETERS --> + <conditional name="ms_amanda"> + <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MS Amanda: Generate Decoys" help="generate decoys" /> + <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select" + help="MS Amanda instrument id option. Available ion types are listed here."> + + <option value="b, y" selected="True">b, y</option> + <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option> + <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option> + <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option> + <option value="a, b, y" >a, b, y</option> + <option value="a, b, y, Imm" >a, b, y, Imm</option> + <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option> + <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option> + <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option> + <option value="b, y, INT" >b, y, INT</option> + <option value="b, y, INT, Imm" >b, y, INT, Imm</option> + <option value="a, b, y, INT" >a, b, y, INT</option> + <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option> + <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option> + <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option> + <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option> + + </param> + <param name="ms_amanda_max_rank" type="integer" value="10" + label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> + <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> + </when> + </conditional> + - <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" - label="Add missing spectrum titles" help="(-missing_titles)"/> + <!-- TIDE ADVANCED PARAMETERS --> + <conditional name="tide"> + <param name="tide_advanced" type="select" label="TIDE Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="tide_num_ptms" type="integer" value="" optional="true" + label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> + <param name="tide_num_ptms_per_type" type="integer" value="2" + label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> + <param name="tide_min_pep_length" type="integer" value="6" + label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> + <param name="tide_max_pep_length" type="integer" value="30" + label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/> + <param name="tide_min_prec_mass" type="float" value="200.0" + label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/> + <param name="tide_max_prec_mass" type="float" value="7200.0" + label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/> + <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences"> + <option value="none" selected="True">none</option> + <option value="shuffle" >shuffle</option> + <option value="peptide-revers" >peptide-reverse</option> + <option value="protein-reverse" >protein-reverse</option> + </param> + <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys"> + <option value="N" >N</option> + <option value="C" >C</option> + <option value="NC" selected="True">NC</option> + <option value="non" >none</option> + </param> + <param name="tide_decoy_seed" type="integer" value="1" + label="TIDE: Decoy Seed" help="Set the decoy seed"/> + <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> + <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> + <option value="0" >0</option> + <option value="10" >10</option> + <option value="20" >20</option> + <option value="30" selected="True">30</option> + <option value="40" >40</option> + <option value="50" >50</option> + <option value="60" >60</option> + </param> - <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="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/> + <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/> + <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules"> + <option value="full-digest" selected="True">full-digest</option> + <option value="partial-digest" >partial-digest</option> + </param> + <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute SP" help="If true, the SP-score is calculated"/> + <param name="tide_max_psms" type="integer" value="10" + label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> + <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> + <param name="tide_min_spectrum_mz" type="float" value="0.0" + label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_max_spectrum_mz" type="float" value="" optional="true" + label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_min_spectrum_peaks" type="integer" value="20" + label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> + <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="all" selected="True">all</option> + </param> + <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/> + <param name="tide_remove_prec_tol" type="float" value="1.5" + label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/> + <param name="tide_progress_indicator" type="integer" value="1000" + label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/> + <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/> + <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/> + <param name="tide_mz_bin_width" type="float" value="0.02" + label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> + <param name="tide_mz_bin_offset" type="float" value="0.0" + label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> + <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> + + <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format"> + <option value="tide_export_text" selected="True">Text</option> + <option value="tide_export_sqt" >SQT</option> + <option value="tide_export_pepxml" >pepxml</option> + <option value="tide_export_mzid" >MzIdentML</option> + <option value="tide_export_pin" >Percolator input file</option> + </param> + + <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> + </when> + </conditional> + + + <!-- MyriMatch ADVANCED PARAMETERS --> + <conditional name="myrimatch"> + <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="myrimatch_min_pep_length" type="integer" value="8" + label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" /> + <param name="myrimatch_max_pep_length" type="integer" value="30" + label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> + <param name="myrimatch_min_prec_mass" type="float" value="600.0" + label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" /> + <param name="myrimatch_max_prec_mass" type="float" value="5000.0" + label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" /> + <param name="myrimatch_num_matches" type="integer" value="10" + label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> + <param name="myrimatch_num_ptms" type="integer" value="2" + label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" /> + <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> + <option value="CID" selected="True">CID</option> + <option value="HCD" >HCD</option> + <option value="ETD" >ETD</option> + </param> + <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals"> + <option value="0">None required</option> + <option value="1">At least one</option> + <option value="2" selected="True" >Both</option> + </param> + <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> + <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> + <param name="myrimatch_tic_cutoff" type="float" value="0.98" + label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" /> + <param name="myrimatch_intensity_classes" type="integer" value="3" + label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> + <param name="myrimatch_class_multiplier" type="integer" value="2" + label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> + <param name="myrimatch_num_batches" type="integer" value="50" + label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> + <param name="myrimatch_max_peak" type="integer" value="100" + label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> + </when> + </conditional> + - <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"/> - </when> - </conditional> + <!-- Andromeda ADVANCED PARAMETERS --> + <!-- Windows only + <conditional name="andromeda"> + <param name="andromeda_advanced" type="select" label="Andromeda Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> + <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> + <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> + <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> + <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> + <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> + <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> + <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> + <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> + <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> + <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> + <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > + <option value="CID" selected="true">CID</option> + <option value="HCD">HCD</option> + <option value="EDT">EDT</option> + </param> + <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> + <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> + <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> + <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" /> + </when> + </conditional> + --> + <!-- Comet ADVANCED PARAMETERS --> + <conditional name="comet"> + <param name="comet_advanced" type="select" label="Comet Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <!-- Spectrum Related parameters --> + <conditional name="comet_spectrum"> + <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related"> + <option value="yes">Set Spectrum Parameters</option> + <option value="no" selected="True">Keep Default Spectrum Parameters</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="comet_min_peaks" type="integer" value="10" + label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" /> + <param name="comet_min_peak_int" type="float" value="0.0" + label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" /> + <conditional name="comet_prec"> + <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal"> + <option value="0" selected="True" >off</option> + <option value="1">on</option> + <option value="2">as expected for ETD/ECD spectra</option> + </param> + <when value="0" /> + <when value="1"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + <when value="2"> + <param name="comet_remove_prec_tol" type="float" value="1.5" + label="Comet: Remove Precursor Tolerance" /> + </when> + </conditional> + <param name="comet_clear_mz_range_lower" type="float" value="0.0" + label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" /> + <param name="comet_clear_mz_range_upper" type="float" value="0.0" + label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" /> + </when> + </conditional> + <!-- Search Related parameters --> + <conditional name="comet_search"> + <param name="comet_search_selector" type="select" label="Comet: Search Related"> + <option value="yes">Set Search Parameters</option> + <option value="no" selected="True">Keep Default Search Parameters</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have"> + <option value="1">semi-specific</option> + <option value="2" selected="True">full-enzyme</option> + <option value="8">unspecific N-term</option> + <option value="9">unspecific C-term</option> + </param> + <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> + <option value="0" selected="True">off</option> + <option value="1">-1,0,+1,+2,+3</option> + <option value="2">-8,-4,0,+4,+8</option> + </param> + <param name="comet_min_prec_mass" type="float" value="0.0" + label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> + <param name="comet_max_prec_mass" type="float" value="10000.0" + label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" /> + <param name="comet_num_matches" type="integer" value="10" + label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" /> + <param name="comet_max_frag_charge" type="integer" value="3" + label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" /> + <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" /> + <param name="comet_batch_size" type="integer" value="0" + label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" /> + <param name="comet_num_ptms" type="integer" value="10" + label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> + </when> + </conditional> + <!-- Fragment Ions Related parameters --> + <conditional name="comet_fragment_ions"> + <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related"> + <option value="yes">Set Fragment Ions Parameters</option> + <option value="no" selected="True">Keep Default Fragment Ions Parameters</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="comet_frag_bin_offset" type="float" value="0.4" + label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> + <param name="comet_theoretical_fragment_ions" type="integer" value="0" + label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="directtag"> + <param name="directtag_advanced" type="select" label="DirectTag Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/> + <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/> + <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/> + <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/> + <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/> + <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/> + <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/> + <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/> + <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/> + <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/> + <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/> + <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping"> + <option value="0" selected="true">no deisotoping</option> + <option value="1">precursor only</option> + <option value="2">precursor and candidate</option> + </param> + <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/> + <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/> + <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/> + <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/> + <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/> + <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/> + <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/> + <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/> + </when> + </conditional> + + <conditional name="novor"> + <param name="novor_advanced" type="select" label="Novor Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> + <option value="HCD" selected="True">HCD</option> + <option value="CID">CID</option> + </param> + <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> + <option value="FT" selected="True">FT</option> + <option value="Trap" >Trap</option> + <option value="TOF" >TOF</option> + </param> + </when> + </conditional> + </section> </inputs> <outputs> <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> @@ -230,28 +1091,62 @@ <!-- Test that specifying non-default search engines works --> <test> <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> - <!-- <param name="input_par" value="Identification_Parameters_specific.par"/>--> - <param name="input_zip" value="IdentificationParametersAndFastaSpecific.zip" ftype="zip" /> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> + <param name="xtandem.xtandem_advanced" value="yes"/> + <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> <!-- Test that search works with MSAmanda --> <test> - <param name="peak_lists" value="searchgui_smallspectra.mgf"/> - <!-- <param name="input_par" value="Identification_Parameters_default.par"/>--> - <param name="input_zip" value="IdentificationParametersAndFastaDefault.zip" ftype="zip" /> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> - <output name="searchgui_results" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> + <!-- Test that specifying non-default search engines works using modifications --> + <!-- + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <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="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> + <param name="xtandem.xtandem_advanced" value="yes"/> + <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> + <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> + </test> + --> + <!-- Test that search works with MSAmanda - with modifications --> + <!-- + <test> + <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> + <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> + <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="engines" value="MS_Amanda"/> + <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> + </test> + --> </tests> <help> **What it does** Runs multiple search engines on any number of MGF peak lists using the SearchGUI. - Default: X! Tandem, OMSSA and MS-GF+ are executed. - Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. </help>