Mercurial > repos > jjohnson > peptideshaker
diff ident_params.xml @ 0:8b99cb00e1c4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
| author | jjohnson |
|---|---|
| date | Tue, 15 May 2018 14:50:35 -0400 |
| parents | |
| children | fa76abf69433 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ident_params.xml Tue May 15 14:50:35 2018 -0400 @@ -0,0 +1,1259 @@ +<tool id="ident_params" name="Identification Parameters" version="1.0"> + <description> + Sets the identification parameters to be used in SearchGUI and PeptideShaker apps + </description> + <macros> + <import>macros_basic.xml</import> + </macros> + <requirements> + <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> + <requirement type="package" version="3.0">zip</requirement> + </requirements> + <expand macro="stdio" /> + <command> +<![CDATA[ + #set $temp_stderr = "searchgui_stderr" + #set $bin_dir = "bin" + + mkdir output; + cwd=`pwd`; + export HOME=\$cwd; + + echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; + + ##################################################### + ## generate IdentificationParameters for SearchGUI ## + ##################################################### + (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI + --exec_dir="\$cwd/${bin_dir}" + -out "\$cwd/SEARCHGUI_IdentificationParameters.par" + + ## SPECTRUM MATCHING PARAMETERS + + -db "${input_database}" + + -frag_tol '${spectrum_matching_options.fragment_tol}' + -frag_ppm '${spectrum_matching_options.fragment_tol_units}' + -prec_tol '${spectrum_matching_options.precursor_ion_tol}' + -prec_ppm '${spectrum_matching_options.precursor_ion_tol_units}' + + #if $spectrum_matching_options.digestion.cleavage == 'default': + ## -enzyme "Trysin" + -mc $spectrum_matching_options.digestion.missed_cleavages + #elif $spectrum_matching_options.digestion.cleavage == '0' and len($spectrum_matching_options.digestion.digests) > 0: + #set $enzymes = [] + #set $missed_cleavages = [] + ## #set $specificities = [] + #for $i, $digest in enumerate($spectrum_matching_options.digestion.digests): + #silent $enzymes.append(str($digest.enzyme)) + #silent $missed_cleavages.append(str($digest.missed_cleavages)) + ## #silent $specificities.append(str($digest.specificity)) + #end for + -enzyme "#echo ','.join($enzymes)#" + -mc "#echo ','.join($missed_cleavages)#" + ## -specificity "#echo ','.join($specificities)#" + #else: + -digestion $spectrum_matching_options.digestion.cleavage + #end if + + + #set $fixed_mods_str = $spectrum_matching_options.fixed_modifications or '' + #set $variable_mods_str = $spectrum_matching_options.variable_modifications or '' + #if $fixed_mods_str + -fixed_mods "$fixed_mods_str" + #end if + #if $variable_mods_str + -variable_mods "$variable_mods_str" + #end if + + + -min_charge $spectrum_matching_options.min_charge + -max_charge $spectrum_matching_options.max_charge + -fi $spectrum_matching_options.forward_ion + -ri $spectrum_matching_options.reverse_ion + -min_isotope ${spectrum_matching_options.min_isotope} + -max_isotope ${spectrum_matching_options.max_isotope} + ## these last two both are also present in the app in the import filters section. + + + ## -- ADVANCED PARAMETERS + + ## TODO: SPECTRUM ANNOTATION + + + ## TODO: SEQUENCE MATCHING + + + ## IMPORT FILTERS + + ##if $advanced_options.import_filters_options.filtering_options_selector == "yes": + + -import_peptide_length_min "${advanced_options.import_filters_options.min_peptide_length}" + -import_peptide_length_max "${advanced_options.import_filters_options.max_peptide_length}" + -import_precurosor_mz "${advanced_options.import_filters_options.max_precursor_error}" + -import_precurosor_mz_ppm "${advanced_options.import_filters_options.max_precursor_error_type}" + ##-max_xtandem_e "${advanced_options.import_filters_options.max_xtandem_e}" + ##-max_omssa_e "${advanced_options.import_filters_options.max_omssa_e}" + ##-max_mascot_e "${advanced_options.import_filters_options.max_mascot_e}" + -exclude_unknown_ptms "${advanced_options.import_filters_options.exclude_unknown_ptms}" + + ## end if + + + ## PTM LOCALIZATION + + -ptm_score "${advanced_options.ptm_localization_options.ptm_score.ptm_score_selector}" + #if $advanced_options.ptm_localization_options.ptm_score.ptm_score_selector == 1 + -score_neutral_losses "${advanced_options.ptm_localization_options.ptm_score.neutral_losses}" + #if str($advanced_options.ptm_localization_options.ptm_score.ptm_threshold) != '' + -ptm_threshold "${advanced_options.ptm_localization_options.ptm_score.ptm_threshold}" + #end if + #end if + -ptm_alignment "${advanced_options.ptm_localization_options.ptm_alignment}" + -ptm_sequence_matching_type "${advanced_options.ptm_localization_options.ptm_sequence_matching_type}" + + + ## GENE ANNOTATION + + $advanced_options.gene_annotation_options.use_gene_mapping + #if $advanced_options.gene_annotation_options.use_gene_mapping: + $advanced_options.gene_annotation_options.update_gene_mapping + #else: + -updateGeneMapping 0 + #end if + + + ## TODO: PROTEIN INFERENCE + + + ## TODO: VALIDATION LEVELS + + -protein_fdr "${advanced_options.validation_levels_options.protein_fdr}" + -peptide_fdr "${advanced_options.validation_levels_options.peptide_fdr}" + -psm_fdr "${advanced_options.validation_levels_options.psm_fdr}" + + + ## FRACTION ANALYSIS + + -protein_fraction_mw_confidence "${advanced_options.fraction_analysis_options.protein_fraction_mw_confidence}" + + + ## -- SEARCH ENGINES SPECIFIC PARAMETERS -- + + + ## XTANDEM ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.xtandem.xtandem_advanced == "yes" + + -xtandem_npeaks ${advanced_options.searchengines_advanced_options.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced_options.searchengines_advanced_options.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced_options.searchengines_advanced_options.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced_options.searchengines_advanced_options.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced_options.searchengines_advanced_options.xtandem.xtandem_noise_suppr} + -xtandem_dynamic_range ${advanced_options.searchengines_advanced_options.xtandem.xtandem_dynamic_range} + -xtandem_quick_acetyl ${advanced_options.searchengines_advanced_options.xtandem.xtandem_quick_acetyl} + -xtandem_quick_pyro ${advanced_options.searchengines_advanced_options.xtandem.xtandem_quick_pyro} + -xtandem_stp_bias ${advanced_options.searchengines_advanced_options.xtandem.xtandem_stp_bias} + -xtandem_evalue ${advanced_options.searchengines_advanced_options.xtandem.xtandem_evalue} + -xtandem_output_proteins ${advanced_options.searchengines_advanced_options.xtandem.xtandem_output_proteins} + -xtandem_output_sequences ${advanced_options.searchengines_advanced_options.xtandem.xtandem_output_sequences} + -xtandem_output_spectra ${advanced_options.searchengines_advanced_options.xtandem.xtandem_output_spectra} + ## -xtandem_skyline_path ${advanced_options.searchengines_advanced_options.xtandem.xtandem_skyline_path} + + #if $advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes" + -xtandem_refine 1 + -xtandem_refine_unc ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt} + -xtandem_refine_pot ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_pot} + -xtandem_refine_pot ${advanced_options.searchengines_advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue} + + #end if + #else + -xtandem_output_spectra 1 + #end if + + + ## OMSSA ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.omssa.omssa_advanced == "yes" + -omssa_hitlist_length ${advanced_options.searchengines_advanced_options.omssa.hitlist_length} + -omssa_remove_prec ${advanced_options.searchengines_advanced_options.omssa.remove_precursor} + -omssa_scale_prec ${advanced_options.searchengines_advanced_options.omssa.scale_precursor} + -omssa_estimate_charge ${advanced_options.searchengines_advanced_options.omssa.estimate_charge} + -omssa_memory ${advanced_options.searchengines_advanced_options.omssa.omssa_memory} + -omssa_neutron ${advanced_options.searchengines_advanced_options.omssa.omssa_neutron} + -omssa_low_intensity "${advanced_options.searchengines_advanced_options.omssa.omssa_low_intensity}" + -omssa_high_intensity ${advanced_options.searchengines_advanced_options.omssa.omssa_high_intensity} + -omssa_intensity_incr ${advanced_options.searchengines_advanced_options.omssa.omssa_intensity_incr} + -omssa_single_window_wd ${advanced_options.searchengines_advanced_options.omssa.omssa_single_window_wd} + -omssa_double_window_wd ${advanced_options.searchengines_advanced_options.omssa.omssa_double_window_wd} + -omssa_single_window_pk ${advanced_options.searchengines_advanced_options.omssa.omssa_single_window_pk} + -omssa_double_window_pk ${advanced_options.searchengines_advanced_options.omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${advanced_options.searchengines_advanced_options.omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${advanced_options.searchengines_advanced_options.omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${advanced_options.searchengines_advanced_options.omssa.omssa_min_peaks} + -omssa_methionine ${advanced_options.searchengines_advanced_options.omssa.omssa_methionine} + -omssa_max_ladders ${advanced_options.searchengines_advanced_options.omssa.omssa_max_ladders} + -omssa_max_frag_charge ${advanced_options.searchengines_advanced_options.omssa.omssa_max_frag_charge} + -omssa_fraction ${advanced_options.searchengines_advanced_options.omssa.omssa_fraction} + -omssa_plus_one ${advanced_options.searchengines_advanced_options.omssa.omssa_plus_one} + -omssa_charge ${advanced_options.searchengines_advanced_options.omssa.omssa_charge} + -omssa_prec_per_spectrum ${advanced_options.searchengines_advanced_options.omssa.omssa_prec_per_spectrum} + -omssa_forward ${advanced_options.searchengines_advanced_options.omssa.omssa_forward} + -omssa_rewind ${advanced_options.searchengines_advanced_options.omssa.omssa_rewind} + -omssa_max_frag_series ${advanced_options.searchengines_advanced_options.omssa.omssa_max_frag_series} + -omssa_corr ${advanced_options.searchengines_advanced_options.omssa.omssa_corr} + -omssa_consecutive_p ${advanced_options.searchengines_advanced_options.omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${advanced_options.searchengines_advanced_options.omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${advanced_options.searchengines_advanced_options.omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${advanced_options.searchengines_advanced_options.omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${advanced_options.searchengines_advanced_options.omssa.omssa_max_evalue} + -omssa_hitlist_charge ${advanced_options.searchengines_advanced_options.omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${advanced_options.searchengines_advanced_options.omssa.omssa_min_pep_length} + -omssa_max_pep_length ${advanced_options.searchengines_advanced_options.omssa.omssa_max_pep_length} + -omssa_format ${advanced_options.searchengines_advanced_options.omssa.omssa_format} + #end if + + + ## MSGF+ ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.msgf.msgf_advanced == "yes" + -msgf_decoy ${advanced_options.searchengines_advanced_options.msgf.msgf_decoy} + -msgf_min_pep_length ${advanced_options.searchengines_advanced_options.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced_options.searchengines_advanced_options.msgf.msgf_max_pep_length} + -msgf_termini ${advanced_options.searchengines_advanced_options.msgf.msgf_termini} + -msgf_num_ptms ${advanced_options.searchengines_advanced_options.msgf.msgf_num_ptms} + -msgf_instrument ${advanced_options.searchengines_advanced_options.msgf.msgf_instrument} + -msgf_fragmentation ${advanced_options.searchengines_advanced_options.msgf.msgf_fragmentation} + -msgf_protocol ${advanced_options.searchengines_advanced_options.msgf.msgf_protocol} + -msgf_num_matches ${advanced_options.searchengines_advanced_options.msgf.msgf_num_matches} + -msgf_additional ${advanced_options.searchengines_advanced_options.msgf.msgf_additional} + #end if + + + ## MSAMANDA ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.ms_amanda.ms_amanda_advanced == "yes" + -ms_amanda_decoy ${advanced_options.searchengines_advanced_options.ms_amanda.ms_amanda_decoy} + -ms_amanda_instrument "${advanced_options.searchengines_advanced_options.ms_amanda.ms_amanda_instrument}" + -ms_amanda_max_rank ${advanced_options.searchengines_advanced_options.ms_amanda.ms_amanda_max_rank} + -ms_amanda_mono ${advanced_options.searchengines_advanced_options.ms_amanda.ms_amanda_mono} + #end if + + + ## MYRIMATCH ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.myrimatch.myrimatch_advanced == "yes" + -myrimatch_min_pep_length ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_min_pep_length} + -myrimatch_max_pep_length ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_max_pep_length} + -myrimatch_min_prec_mass ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_min_prec_mass} + -myrimatch_max_prec_mass ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_max_prec_mass} + -myrimatch_num_matches ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_num_matches} + -myrimatch_num_ptms ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_num_ptms} + -myrimatch_fragmentation ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_fragmentation} + -myrimatch_termini ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_termini} + -myrimatch_plus_three ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_plus_three} + -myrimatch_xcorr ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_xcorr} + -myrimatch_tic_cutoff ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_tic_cutoff} + -myrimatch_intensity_classes ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_intensity_classes} + -myrimatch_class_multiplier ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_class_multiplier} + -myrimatch_num_batches ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_num_batches} + -myrimatch_max_peak ${advanced_options.searchengines_advanced_options.myrimatch.myrimatch_max_peak} + #end if + + + ## ANDROMEDA ADVANCED PARAMETERS + + #* Not working in tests + #if $advanced_options.searchengines_advanced_options.andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${advanced_options.searchengines_advanced_options.andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${advanced_options.searchengines_advanced_options.andromeda.andromeda_max_comb} + -andromeda_top_peaks ${advanced_options.searchengines_advanced_options.andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${advanced_options.searchengines_advanced_options.andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${advanced_options.searchengines_advanced_options.andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${advanced_options.searchengines_advanced_options.andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${advanced_options.searchengines_advanced_options.andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${advanced_options.searchengines_advanced_options.andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${advanced_options.searchengines_advanced_options.andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${advanced_options.searchengines_advanced_options.andromeda.andromeda_higher_charge} + -andromeda_equal_il ${advanced_options.searchengines_advanced_options.andromeda.andromeda_equal_il} + -andromeda_frag_method ${advanced_options.searchengines_advanced_options.andromeda.andromeda_frag_method} + -andromeda_max_mods ${advanced_options.searchengines_advanced_options.andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${advanced_options.searchengines_advanced_options.andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${advanced_options.searchengines_advanced_options.andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${advanced_options.searchengines_advanced_options.andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${advanced_options.searchengines_advanced_options.andromeda.andromeda_decoy_mode} + #end if + *# + + + ## TIDE ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.tide.tide_advanced == "yes" + #if str($advanced_options.searchengines_advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_num_ptms ${advanced_options.searchengines_advanced_options.tide.tide_max_spectrum_mz} + #end if + -tide_num_ptms_per_type ${advanced_options.searchengines_advanced_options.tide.tide_num_ptms_per_type} + -tide_min_pep_length ${advanced_options.searchengines_advanced_options.tide.tide_min_pep_length} + -tide_max_pep_length ${advanced_options.searchengines_advanced_options.tide.tide_max_pep_length} + -tide_min_prec_mass ${advanced_options.searchengines_advanced_options.tide.tide_min_prec_mass} + -tide_max_prec_mass ${advanced_options.searchengines_advanced_options.tide.tide_max_prec_mass} + -tide_decoy_format ${advanced_options.searchengines_advanced_options.tide.tide_decoy_format} + -tide_keep_terminals ${advanced_options.searchengines_advanced_options.tide.tide_keep_terminals} + -tide_print_peptides ${advanced_options.searchengines_advanced_options.tide.tide_print_peptides} + -tide_verbosity ${advanced_options.searchengines_advanced_options.tide.tide_verbosity} + -tide_monoisotopic ${advanced_options.searchengines_advanced_options.tide.tide_monoisotopic} + -tide_clip_n_term ${advanced_options.searchengines_advanced_options.tide.tide_clip_n_term} + -tide_digestion_type ${advanced_options.searchengines_advanced_options.tide.tide_digestion_type} + -tide_compute_sp ${advanced_options.searchengines_advanced_options.tide.tide_compute_sp} + -tide_max_psms ${advanced_options.searchengines_advanced_options.tide.tide_max_psms} + -tide_compute_p ${advanced_options.searchengines_advanced_options.tide.tide_compute_p} + -tide_min_spectrum_mz ${advanced_options.searchengines_advanced_options.tide.tide_min_spectrum_mz} + #if str($advanced_options.searchengines_advanced_options.tide.tide_max_spectrum_mz).strip() != '': + -tide_max_spectrum_mz ${advanced_options.searchengines_advanced_options.tide.tide_max_spectrum_mz} + #end if + -tide_min_spectrum_peaks ${advanced_options.searchengines_advanced_options.tide.tide_min_spectrum_peaks} + -tide_spectrum_charges ${advanced_options.searchengines_advanced_options.tide.tide_spectrum_charges} + -tide_remove_prec ${advanced_options.searchengines_advanced_options.tide.tide_remove_prec} + -tide_remove_prec_tol ${advanced_options.searchengines_advanced_options.tide.tide_remove_prec_tol} + -tide_progress_indicator ${advanced_options.searchengines_advanced_options.tide.tide_progress_indicator} + -tide_use_flanking ${advanced_options.searchengines_advanced_options.tide.tide_use_flanking} + -tide_use_neutral_losses ${advanced_options.searchengines_advanced_options.tide.tide_use_neutral_losses} + -tide_mz_bin_width ${advanced_options.searchengines_advanced_options.tide.tide_mz_bin_width} + -tide_mz_bin_offset ${advanced_options.searchengines_advanced_options.tide.tide_mz_bin_offset} + -tide_concat ${advanced_options.searchengines_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.searchengines_advanced_options.tide.tide_export).strip() == $format: + -$format 1 + #else: + -$format 0 + #end if + + #end for + + -tide_remove_temp ${advanced_options.searchengines_advanced_options.tide.tide_remove_temp} + + #end if + + + ## COMET ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.comet.comet_advanced == "yes" + + #if $advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" + -comet_min_peaks ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_min_peaks} + -comet_min_peak_int ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_min_peak_int} + + -comet_remove_prec ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec} + + + #if $advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #end if + + #if $advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #end if + + -comet_clear_mz_range_lower ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower} + -comet_clear_mz_range_upper ${advanced_options.searchengines_advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper} + #end if + + #if $advanced_options.searchengines_advanced_options.comet.comet_search.comet_search_selector == "yes" + -comet_enzyme_type ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_enzyme_type} + -comet_isotope_correction ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_isotope_correction} + -comet_min_prec_mass ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_min_prec_mass} + -comet_max_prec_mass ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_max_prec_mass} + -comet_num_matches ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_num_matches} + -comet_max_frag_charge ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_max_frag_charge} + -comet_remove_meth ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_remove_meth} + -comet_batch_size ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_batch_size} + -comet_num_ptms ${advanced_options.searchengines_advanced_options.comet.comet_search.comet_num_ptms} + #end if + + #if $advanced_options.searchengines_advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" + -comet_frag_bin_offset ${advanced_options.searchengines_advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset} + -comet_theoretical_fragment_ions ${advanced_options.searchengines_advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} + #end if + #end if + + + ## DIRECTTAG ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${advanced_options.searchengines_advanced_options.directtag.directag_tic_cutoff} + -directag_max_peak_count ${advanced_options.searchengines_advanced_options.directtag.directag_max_peak_count} + -directag_intensity_classes ${advanced_options.searchengines_advanced_options.directtag.directag_intensity_classes} + -directag_adjust_precursor ${advanced_options.searchengines_advanced_options.directtag.directag_adjust_precursor} + -directag_min_adjustment ${advanced_options.searchengines_advanced_options.directtag.directag_min_adjustment} + -directag_max_adjustment ${advanced_options.searchengines_advanced_options.directtag.directag_max_adjustment} + -directag_adjustment_step ${advanced_options.searchengines_advanced_options.directtag.directag_adjustment_step} + -directag_charge_states ${advanced_options.searchengines_advanced_options.directtag.directag_charge_states} + #if str($advanced_options.searchengines_advanced_options.directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${advanced_options.searchengines_advanced_options.directtag.directag_output_suffix} + #end if + -directag_ms_charge_state ${advanced_options.searchengines_advanced_options.directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${advanced_options.searchengines_advanced_options.directtag.directag_duplicate_spectra} + -directag_deisotoping ${advanced_options.searchengines_advanced_options.directtag.directag_deisotoping} + -directag_isotope_tolerance ${advanced_options.searchengines_advanced_options.directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${advanced_options.searchengines_advanced_options.directtag.directag_complement_tolerance} + -directag_tag_length ${advanced_options.searchengines_advanced_options.directtag.directag_tag_length} + -directag_max_var_mods ${advanced_options.searchengines_advanced_options.directtag.directag_max_var_mods} + -directag_max_tag_count ${advanced_options.searchengines_advanced_options.directtag.directag_max_tag_count} + -directag_intensity_weight ${advanced_options.searchengines_advanced_options.directtag.directag_intensity_weight} + -directag_fidelity_weight ${advanced_options.searchengines_advanced_options.directtag.directag_fidelity_weight} + -directag_complement_weight ${advanced_options.searchengines_advanced_options.directtag.directag_complement_weight} + #end if + + + ## NOVOR ADVANCED PARAMETERS + + #if $advanced_options.searchengines_advanced_options.novor.novor_advanced == "yes" + -novor_fragmentation ${advanced_options.searchengines_advanced_options.novor.novor_fragmentation} + -novor_mass_analyzer ${advanced_options.searchengines_advanced_options.novor.novor_mass_analyzer} + #end if + + 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"/> + + <!-- General Parameters --> + <!-- <expand macro="general_options"/>--> + + <!-- SPECTRUM MATCHING PARAMETERS --> + + <section name="spectrum_matching_options" expanded="false" title="Spectrum Matching Options"> + + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + + <conditional name="digestion"> + <param name="cleavage" type="select" label="Digestion"> + <option value="default" selected="true">Trypsin</option> + <option value="0">Select Enzymes</option> + <option value="1">Unspecific Cleavage</option> + <option value="2">Whole Protein</option> + </param> + <when value="default"> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + </when> + <when value="0"> + <repeat name="digests" min="1" title="Enzymes"> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="Whole Protein">Whole Protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + <option value="LysargiNase">LysargiNase</option> + <option value="Semi-LysargiNase">Semi-LysargiNase</option> + <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> + <option value="Semi-Arg-C">Semi-Arg-C</option> + <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> + <option value="Arg-N">Arg-N</option> + <option value="Semi-Arg-N">Semi-Arg-N</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + <!-- + <param name="specificity" type="select" label="Specificity"> + <option value="0" selected="true">Specific at both termini</option> + <option value="1">Semi-Specific - one terminus</option> + <option value="2">Specific at the N-terminus only</option> + <option value="3">Specific at the C-terminus only</option> + </param> + --> + </repeat> + </when> + <when value="1"/> + <when value="2"/> + </conditional> + + <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" + help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> + <option value="1">Parts per million (ppm)</option> + <option value="0">Daltons</option> + </param> + <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance" + help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> + <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" + help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> + <option value="1">Parts per million (ppm)</option> + <option value="0" selected="true">Daltons</option> + </param> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" + help="Provide error value for fragment ions, based on instrument used"/> + <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> + <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> + <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> + </section> + + + <!-- ADVANCED PARAMETERS --> + + <!-- TODO: SPECTRUM ANNOTATION --> + + + <!-- TODO: SEQUENCE MATCHING --> + + <section name="advanced_options" expanded="false" title="Show/Hide advanced options"> + + <section name="import_filters_options" expanded="false" title="Import filters"> + <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="8" /> + <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" /> + <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10" + help="Next option specifies units (Da or ppm)" /> + <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select"> + <option value="1">ppm</option> + <option value="0">Daltons</option> + </param> + <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /--> + <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> + <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> + <!-- TODO: import_missed_cleavages_min, import_missed_cleavages_max --> + <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + </section> + + + <!-- PTM LOCALIZATION --> + + <section name="ptm_localization_options" expanded="false" title="PTM Localizacion"> + <conditional name="ptm_score"> + <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization"> + <option value="0" >A-score</option> + <option value="1" selected="True">PhosphoRS</option> + <option value="2">None</option> + </param> + <when value="0" /> + <when value="1"> + <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" /> + <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float" + help="Automatic mode will be used if not set" /> + </when> + <when value="2" /> + </conditional> + <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type"> + <option value="0">Character Sequence</option> + <option value="1" selected="true">Amino Acids</option> + <option value="2">Indistinguishable Amino Acids</option> + </param> + <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/> + </section> + + + <!-- GENE ANNOTATION --> + + <section name="gene_annotation_options" expanded="false" title="Gene Annotation"> + <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> + + + <!-- TODO: PROTEIN INFERENCE --> + + + <!-- VALIDATION LEVELS --> + + + <section name="validation_levels_options" expanded="false" title="Validation Levels"> + <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" /> + <!-- TODO: to include, at least, group_psms; look into group_peptides and merge_subgroups --> + </section> + + + <!-- FRACTION ANALYSIS --> + + + <section name="fraction_analysis_options" expanded="false" title="Fraction Analysis"> + <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot" + help="default 95%: '95.0'" /> + <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} --> + </section> + + + <!-- - ADVANCED SEARCH ENGINES OPTIONS --> + + <section name="searchengines_advanced_options" expanded="false" title="Search Engines"> + + <!-- 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> + + + <!-- 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="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> + + + <!-- 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> + </section> + + </inputs> + <outputs> + <data name="Searchgui_Identification_Parameters" format="par" from_work_dir="SEARCHGUI_IdentificationParameters.par" label="${tool.name}: PAR file on ${on_string}" /> + </outputs> + <tests> + + <!-- Test that default parameters generates a standar par file --> + <test> + <param name="input_database" value="searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta"/> + <output name="Searchgui_Identification_Parameters" file="Identification_Parameters_default.par" ftype="par" compare="sim_size" delta="1000" /> + </test> + <!-- Test specific parameters --> + <test> + <param name="input_database" value="searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta"/> + <param name="precursor_ion_tol" value="100"/> + <param name="fixed_modifications" value="Carbamidomethylation of C"/> + <param name="variable_modifications" value="Oxidation of M"/> + <param name="min_charge" value="1"/> + <param name="max_charge" value="3"/> + <param name="xtandem_advanced" value="yes"/> + <param name="xtandem_refine_selector" value="yes"/> + <output name="Searchgui_Identification_Parameters" file="Identification_Parameters_specific.par" ftype="par" compare="sim_size" delta="5000" /> + </test> + + </tests> + <help> +**What it does** + +Creates a parameters file which can be used independently by SearchGUI or PeptideShaker apps. + +FASTA file used by this app must be kept in the history as the generated .par file will reference to it. + +A FASTA file with decoy sequences is recommended if SearchGUI and PeptideShaker are going to be used. + + </help> + <expand macro="citations" /> +</tool>