peptideshaker: searchgui.xml comparison

comparison searchgui.xml @ 33:bce45e9e6d70 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312

author	galaxyp
date	Mon, 06 Feb 2017 21:53:07 -0500
parents	ff592231f118
children	5a38c0d33704

comparison

equal deleted inserted replaced

-:ff592231f118
+:bce45e9e6d70
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
 <description>
 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
 </description>
 <macros>
 <import>macros.xml</import>
 mkdir output_reports;
 cwd=`pwd`;
 export HOME=\$cwd;
 ## echo the search engines to run
-echo "$engines";
+echo "$search_engines_options.engines";
 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
 cp "${input_database}" input_database.fasta;
 ###########################################
 ####       Creating decoy database     ####
 ###########################################
-#if $create_decoy:
+#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;
 -out SEARCHGUI_IdentificationParameters.par
 @GENERAL_PARAMETERS@
 -db input_database.fasta
-#if $use_gene_mapping:
+#if $protein_database_options.use_gene_mapping:
-$use_gene_mapping
+$protein_database_options.use_gene_mapping
-$update_gene_mapping
+$protein_database_options.update_gene_mapping
 #end if
-#if $xtandem.xtandem_advanced == "yes"
+#if $advanced_options.xtandem.xtandem_advanced == "yes"
--xtandem_npeaks ${xtandem.xtandem_npeaks}
+-xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
--xtandem_min_peaks ${xtandem.xtandem_min_peaks}
+-xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
--xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}
+-xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
--xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}
+-xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
--xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}
+-xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
--xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}
+-xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
--xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl}
+-xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
--xtandem_quick_pyro ${xtandem.xtandem_quick_pyro}
+-xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
--xtandem_stp_bias ${xtandem.xtandem_stp_bias}
+-xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
--xtandem_evalue ${xtandem.xtandem_evalue}
+-xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
--xtandem_output_proteins ${xtandem.xtandem_output_proteins}
+-xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
--xtandem_output_sequences ${xtandem.xtandem_output_sequences}
+-xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
--xtandem_output_spectra ${xtandem.xtandem_output_spectra}
+-xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
-## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}
+## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
-#if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+#if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
 -xtandem_refine 1
--xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}
+-xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
--xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}
+-xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
--xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}
+-xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
--xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}
+-xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
--xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
+-xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
--xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
+-xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
--xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
+-xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
 #end if
 #else
 -xtandem_output_spectra 1
 #end if
-#if $omssa.omssa_advanced == "yes"
+#if $advanced_options.omssa.omssa_advanced == "yes"
--omssa_hitlist_length ${omssa.hitlist_length}
+-omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
--omssa_remove_prec ${omssa.remove_precursor}
+-omssa_remove_prec ${advanced_options.omssa.remove_precursor}
--omssa_scale_prec ${omssa.scale_precursor}
+-omssa_scale_prec ${advanced_options.omssa.scale_precursor}
--omssa_estimate_charge ${omssa.estimate_charge}
+-omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
--omssa_memory ${omssa.omssa_memory}
+-omssa_memory ${advanced_options.omssa.omssa_memory}
--omssa_neutron ${omssa.omssa_neutron}
+-omssa_neutron ${advanced_options.omssa.omssa_neutron}
--omssa_low_intensity "${omssa.omssa_low_intensity}"
+-omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
--omssa_high_intensity ${omssa.omssa_high_intensity}
+-omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
--omssa_intensity_incr ${omssa.omssa_intensity_incr}
+-omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
--omssa_single_window_wd ${omssa.omssa_single_window_wd}
+-omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
--omssa_double_window_wd ${omssa.omssa_double_window_wd}
+-omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
--omssa_single_window_pk ${omssa.omssa_single_window_pk}
+-omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
--omssa_double_window_pk ${omssa.omssa_double_window_pk}
+-omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
--omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks}
+-omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
--omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks}
+-omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
--omssa_min_peaks ${omssa.omssa_min_peaks}
+-omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
--omssa_methionine ${omssa.omssa_methionine}
+-omssa_methionine ${advanced_options.omssa.omssa_methionine}
--omssa_max_ladders ${omssa.omssa_max_ladders}
+-omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
--omssa_max_frag_charge ${omssa.omssa_max_frag_charge}
+-omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
--omssa_fraction ${omssa.omssa_fraction}
+-omssa_fraction ${advanced_options.omssa.omssa_fraction}
--omssa_plus_one ${omssa.omssa_plus_one}
+-omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
--omssa_charge ${omssa.omssa_charge}
+-omssa_charge ${advanced_options.omssa.omssa_charge}
--omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum}
+-omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
--omssa_forward ${omssa.omssa_forward}
+-omssa_forward ${advanced_options.omssa.omssa_forward}
--omssa_rewind ${omssa.omssa_rewind}
+-omssa_rewind ${advanced_options.omssa.omssa_rewind}
--omssa_max_frag_series ${omssa.omssa_max_frag_series}
+-omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
--omssa_corr ${omssa.omssa_corr}
+-omssa_corr ${advanced_options.omssa.omssa_corr}
--omssa_consecutive_p ${omssa.omssa_consecutive_p}
+-omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
--omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue}
+-omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
--omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue}
+-omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
--omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue}
+-omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
--omssa_max_evalue ${omssa.omssa_max_evalue}
+-omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
--omssa_hitlist_charge ${omssa.omssa_hitlist_charge}
+-omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
--omssa_min_pep_length ${omssa.omssa_min_pep_length}
+-omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
--omssa_max_pep_length ${omssa.omssa_max_pep_length}
+-omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
--omssa_format ${omssa.omssa_format}
+-omssa_format ${advanced_options.omssa.omssa_format}
 #end if
-#if $msgf.msgf_advanced == "yes"
+#if $advanced_options.msgf.msgf_advanced == "yes"
--msgf_decoy ${msgf.msgf_decoy}
+-msgf_decoy ${advanced_options.msgf.msgf_decoy}
--msgf_min_pep_length ${msgf.msgf_min_pep_length}
+-msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
--msgf_max_pep_length ${msgf.msgf_max_pep_length}
+-msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
--msgf_termini ${msgf.msgf_termini}
+-msgf_termini ${advanced_options.msgf.msgf_termini}
--msgf_num_ptms ${msgf.msgf_num_ptms}
+-msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
--msgf_instrument ${msgf.msgf_instrument}
+-msgf_instrument ${advanced_options.msgf.msgf_instrument}
--msgf_fragmentation ${msgf.msgf_fragmentation}
+-msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
--msgf_protocol ${msgf.msgf_protocol}
+-msgf_protocol ${advanced_options.msgf.msgf_protocol}
--msgf_num_matches ${msgf.msgf_num_matches}
+-msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
--msgf_additional ${msgf.msgf_additional}
+-msgf_additional ${advanced_options.msgf.msgf_additional}
 #end if
 #* Not working in tests
-#if $ms_amanda.ms_amanda_advanced == "yes"
+#if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
--ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
+-ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
--ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
+-ms_amanda_max_evalue ${advanced_options.ms_amanda.ms_amanda_max_evalue}
--ms_amanda_instrument ${ms_amanda.ms_amanda_instrument}
+-ms_amanda_instrument ${advanced_options.ms_amanda.ms_amanda_instrument}
--ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank}
+-ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
--ms_amanda_mono ${ms_amanda.ms_amanda_mono}
+-ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
 #end if
 *#
 #* Not working in tests
-#if $myrimatch.myrimatch_advanced == "yes"
+#if $advanced_options.myrimatch.myrimatch_advanced == "yes"
--myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
+-myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
--myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
+-myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
--myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
+-myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
--myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
+-myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
--myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
+-myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
--myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
+-myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
--myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
+-myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
--myrimatch_termini ${myrimatch.myrimatch_termini}
+-myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
--myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
+-myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
--myrimatch_xcorr ${myrimatch.myrimatch_xcorr}
+-myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
--myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff}
+-myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
--myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
+-myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
--myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
+-myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
--myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
+-myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
--myrimatch_max_peak ${myrimatch.myrimatch_max_peak}
+-myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
 #end if
 *#
 #* Not working in tests
-#if $andromeda.andromeda_advanced == "yes"
+#if $advanced_options.andromeda.andromeda_advanced == "yes"
--andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
+-andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
--andromeda_max_comb ${andromeda.andromeda_max_comb}
+-andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
--andromeda_top_peaks ${andromeda.andromeda_top_peaks}
+-andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
--andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window}
+-andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
--andromeda_incl_water ${andromeda.andromeda_incl_water}
+-andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
--andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia}
+-andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
--andromeda_neutral_losses ${andromeda.andromeda_neutral_losses}
+-andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
--andromeda_fragment_all ${andromeda.andromeda_fragment_all}
+-andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
--andromeda_emp_correction ${andromeda.andromeda_emp_correction}
+-andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
--andromeda_higher_charge ${andromeda.andromeda_higher_charge}
+-andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
--andromeda_equal_il ${andromeda.andromeda_equal_il}
+-andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
--andromeda_frag_method ${andromeda.andromeda_frag_method}
+-andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
--andromeda_max_mods ${andromeda.andromeda_max_mods}
+-andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
--andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
+-andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
--andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
+-andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
--andromeda_max_psms ${andromeda.andromeda_max_psms}
+-andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
--andromeda_decoy_mode ${andromeda.andromeda_decoy_mode}
+-andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
 #end if
 *#
 #* Not working in tests
-#if $tide.tide_advanced == "yes"
+#if $advanced_options.tide.tide_advanced == "yes"
--tide_num_ptms ${tide.tide_num_ptms}
+-tide_num_ptms ${advanced_options.tide.tide_num_ptms}
--tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
+-tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
--tide_min_pep_length ${tide.tide_min_pep_length}
+-tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
--tide_max_pep_length ${tide.tide_max_pep_length}
+-tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
--tide_min_prec_mass ${tide.tide_min_prec_mass}
+-tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
--tide_max_prec_mass ${tide.tide_max_prec_mass}
+-tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
--tide_decoy_format ${tide.tide_decoy_format}
+-tide_decoy_format ${advanced_options.tide.tide_decoy_format}
--tide_keep_terminals ${tide.tide_keep_terminals}
+-tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
--tide_output_folder ${tide.tide_output_folder}
+-tide_output_folder ${advanced_options.tide.tide_output_folder}
--tide_print_peptides ${tide.tide_print_peptides}
+-tide_print_peptides ${advanced_options.tide.tide_print_peptides}
--tide_verbosity ${tide.tide_verbosity}
+-tide_verbosity ${advanced_options.tide.tide_verbosity}
--tide_monoisotopic ${tide.tide_monoisotopic}
+-tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
--tide_clip_n_term ${tide.tide_clip_n_term}
+-tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
--tide_digestion_type ${tide.tide_digestion_type}
+-tide_digestion_type ${advanced_options.tide.tide_digestion_type}
--tide_compute_sp ${tide.tide_compute_sp}
+-tide_compute_sp ${advanced_options.tide.tide_compute_sp}
--tide_max_psms ${tide.tide_max_psms}
+-tide_max_psms ${advanced_options.tide.tide_max_psms}
--tide_compute_p ${tide.tide_compute_p}
+-tide_compute_p ${advanced_options.tide.tide_compute_p}
--tide_min_spectrum_mz ${tide.tide_min_spectrum_mz}
+-tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
--tide_max_spectrum_mz ${tide.tide_max_spectrum_mz}
+-tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
--tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks}
+-tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
--tide_spectrum_charges ${tide.tide_spectrum_charges}
+-tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
--tide_remove_prec ${tide.tide_remove_prec}
+-tide_remove_prec ${advanced_options.tide.tide_remove_prec}
--tide_remove_prec_tol ${tide.tide_remove_prec_tol}
+-tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
--tide_progress_indicator ${tide.tide_progress_indicator}
+-tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
--tide_use_flanking ${tide.tide_use_flanking}
+-tide_use_flanking ${advanced_options.tide.tide_use_flanking}
--tide_use_neutral_losses ${tide.tide_use_neutral_losses}
+-tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
--tide_mz_bin_width ${tide.tide_mz_bin_width}
+-tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
--tide_mz_bin_offset ${tide.tide_mz_bin_offset}
+-tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
--tide_concat ${tide.tide_concat}
+-tide_concat ${advanced_options.tide.tide_concat}
--tide_export_text ${tide.tide_export_text}
+-tide_export_text ${advanced_options.tide.tide_export_text}
--tide_export_sqt ${tide.tide_export_sqt}
+-tide_export_sqt ${advanced_options.tide.tide_export_sqt}
--tide_export_pepxml ${tide.tide_export_pepxml}
+-tide_export_pepxml ${advanced_options.tide.tide_export_pepxml}
--tide_export_mzid ${tide.tide_export_mzid}
+-tide_export_mzid ${advanced_options.tide.tide_export_mzid}
--tide_export_pin ${tide.tide_export_pin}
+-tide_export_pin ${advanced_options.tide.tide_export_pin}
--tide_remove_temp ${tide.tide_remove_temp}
+-tide_remove_temp ${advanced_options.tide.tide_remove_temp}
 #end if
 *#
-#if $comet.comet_advanced == "yes"
+#if $advanced_options.comet.comet_advanced == "yes"
-#if $comet.comet_spectrum.comet_spectrum_selector == "yes"
+#if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
--comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
+-comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
--comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
+-comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
--comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec}
+-comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
-#if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
+#if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
--comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+-comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
 #end if
-#if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
+#if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
--comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
+-comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
 #end if
--comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
+-comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
--comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
+-comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
 #end if
-#if $comet.comet_search.comet_search_selector == "yes"
+#if $advanced_options.comet.comet_search.comet_search_selector == "yes"
--comet_enzyme_type ${comet.comet_search.comet_enzyme_type}
+-comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
--comet_isotope_correction ${comet.comet_search.comet_isotope_correction}
+-comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
--comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass}
+-comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
--comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass}
+-comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
--comet_num_matches ${comet.comet_search.comet_num_matches}
+-comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
--comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge}
+-comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
--comet_remove_meth ${comet.comet_search.comet_remove_meth}
+-comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
--comet_batch_size ${comet.comet_search.comet_batch_size}
+-comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
--comet_num_ptms ${comet.comet_search.comet_num_ptms}
+-comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
 #end if
-#if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
+#if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
--comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset}
+-comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
--comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
+-comet_sparse_matrix ${advanced_options.comet.comet_fragment_ions.comet_sparse_matrix}
--comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
+-comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
 #end if
 #end if
-#if $directtag.directtag_advanced == "yes"
+#if $advanced_options.directtag.directtag_advanced == "yes"
--directag_tic_cutoff ${directtag.directag_tic_cutoff}
+-directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
--directag_max_peak_count ${directtag.directag_max_peak_count}
+-directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
--directag_intensity_classes ${directtag.directag_intensity_classes}
+-directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
--directag_adjust_precursor ${directtag.directag_adjust_precursor}
+-directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
--directag_min_adjustment ${directtag.directag_min_adjustment}
+-directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
--directag_max_adjustment ${directtag.directag_max_adjustment}
+-directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
--directag_adjustment_step ${directtag.directag_adjustment_step}
+-directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
--directag_charge_states ${directtag.directag_charge_states}
+-directag_charge_states ${advanced_options.directtag.directag_charge_states}
-#if str($directtag.directag_output_suffix).strip() != '':
+#if str($advanced_options.directtag.directag_output_suffix).strip() != '':
--directag_output_suffix ${directtag.directag_output_suffix}
+-directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
 #end if
--directag_ms_charge_state ${directtag.directag_ms_charge_state}
+-directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
--directag_duplicate_spectra ${directtag.directag_duplicate_spectra}
+-directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
--directag_deisotoping ${directtag.directag_deisotoping}
+-directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
--directag_isotope_tolerance ${directtag.directag_isotope_tolerance}
+-directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
--directag_complement_tolerance ${directtag.directag_complement_tolerance}
+-directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
--directag_tag_length ${directtag.directag_tag_length}
+-directag_tag_length ${advanced_options.directtag.directag_tag_length}
--directag_max_var_mods ${directtag.directag_max_var_mods}
+-directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
--directag_max_tag_count ${directtag.directag_max_tag_count}
+-directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
--directag_intensity_weight ${directtag.directag_intensity_weight}
+-directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
--directag_fidelity_weight ${directtag.directag_fidelity_weight}
+-directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
--directag_complement_weight ${directtag.directag_complement_weight}
+-directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
 #end if
-#if $novor.novor_advanced == "yes"
+#if $advanced_options.novor.novor_advanced == "yes"
--novor_fragmentation ${novor.novor_fragmentation}
+-novor_fragmentation ${advanced_options.novor.novor_fragmentation}
--novor_mass_analyzer ${novor.novor_mass_analyzer}
+-novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
 #end if
 2> $temp_stderr)
 &&
 -output_folder \$cwd/output
 -id_params SEARCHGUI_IdentificationParameters.par
 -threads "\${GALAXY_SLOTS:-12}"
-#if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
+#if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
--correct_titles "${searchgui_advanced.correct_titles}"
+-correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
-$searchgui_advanced.missing_titles
+$advanced_options.searchgui_advanced.missing_titles
--mgf_splitting "${searchgui_advanced.mgf_splitting}"
+-mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
--mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
+-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
 ## the tree is generated afterwards in PeptideShaker
 ## -protein_index 0
 ##-makeblastdb_folder \$BLAST_ROOT_DIR
-#set $engines_list = str($engines).split(',')
+#set $engines_list = str($search_engines_options.engines).split(',')
 #if 'X!Tandem' in $engines_list:
 -xtandem 1
 #else
 -xtandem 0
 #end if
 </command>
 <inputs>
 <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"
-<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)"
-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" />
-<param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
+</section>
-label="Update gene mappings automatically from Ensembl (UniProt databases only)"
-help="This should only be enabled for UniProt databaases" />
 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
 help="Select appropriate MGF dataset(s) from history" />
 <!-- Search Engine Selection -->
-<param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
+<section name="search_engines_options" expanded="false" title="Search Engine Options">
-<help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
+<param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
-<option value="X!Tandem" selected="True">X!Tandem</option>
+<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="MSGF" selected="True">MS-GF+</option>
-<option value="Comet">Comet</option>
+<option value="OMSSA" selected="True">OMSSA</option>
-<!-- Not working in tests
+<option value="Comet">Comet</option>
--->
+<!-- Not working in tests
-<option value="Tide">Tide</option>
+-->
-<!-- Not working in tests
+<option value="Tide">Tide</option>
--->
+<!-- Not working in tests
-<option value="MyriMatch">MyriMatch</option>
+-->
-<option value="MS_Amanda">MS_Amanda</option>
+<option value="MyriMatch">MyriMatch</option>
-<!-- Windows only
+<option value="MS_Amanda">MS_Amanda</option>
-<option value="Andromeda">Andromeda</option>
+<!-- Windows only
--->
+<option value="Andromeda">Andromeda</option>
-<!-- New with version 3.0
+-->
--->
+<!-- New with version 3.0
-<!--working in tests
+-->
--->
+<!--working in tests
-<option value="DirecTag">DirecTag</option>
+-->
-<option value="Novor">Novor (Select for non-commercial use only)</option>
+<option value="DirecTag">DirecTag</option>
-<validator type="no_options" message="Please select at least one output file" />
+<option value="Novor">Novor (Select for non-commercial use only)</option>
-</param>
+<validator type="no_options" message="Please select at least one output file" />
+</param>
+</section>
 <!-- General Parameters -->
 <expand macro="general_options"/>
-<!-- Optional Advanced SearchGUI Parameters -->
-<conditional name="searchgui_advanced">
+<section name="advanced_options" expanded="false" title="Andvanced Options">
-<param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
+<!-- Optional Advanced SearchGUI Parameters -->
-<option value="basic" selected="True">Default</option>
+<conditional name="searchgui_advanced">
-<option value="advanced">Advanced</option>
+<param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
-</param>
+<option value="basic" selected="True">Default</option>
-<when value="basic" />
+<option value="advanced">Advanced</option>
-<when value="advanced">
+</param>
-<param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
+<when value="basic" />
-help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
+<when value="advanced">
-<option value="0">no correction</option>
+<param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
-<option value="1" selected="True">rename spectra</option>
+help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
-<option value="2">delete spectra</option>
+<option value="0">no correction</option>
-</param>
+<option value="1" selected="True">rename spectra</option>
+<option value="2">delete spectra</option>
-<param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
+</param>
-label="Add missing spectrum titles" help="(-missing_titles)"/>
+<param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
-<param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
+label="Add missing spectrum titles" help="(-missing_titles)"/>
-help="Choose a smaller value if you are running on a machine with limited memory"/>
+<param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
-<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"/>
-help="Choose a smaller value if you are running on a machine with limited memory"/>
-</when>
+<param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
-</conditional>
+help="Choose a smaller value if you are running on a machine with limited memory"/>
+</when>
+</conditional>
-<!-- X!TANDEM ADVANCED PARAMETERS -->
-<conditional name="xtandem">
+<!-- X!TANDEM ADVANCED PARAMETERS -->
-<param name="xtandem_advanced" type="select" label="X!Tandem Options">
+<conditional name="xtandem">
-<option value="yes">Advanced</option>
+<param name="xtandem_advanced" type="select" label="X!Tandem Options">
-<option value="no" selected="True">Default</option>
+<option value="yes">Advanced</option>
-</param>
+<option value="no" selected="True">Default</option>
-<when value="no" />
+</param>
-<when value="yes">
+<when value="no" />
-<param name="xtandem_npeaks" type="integer" value="50"
+<when value="yes">
-label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
+<param name="xtandem_npeaks" type="integer" value="50"
-<param name="xtandem_min_peaks" type="integer" value="15"
+label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
-label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
+<param name="xtandem_min_peaks" type="integer" value="15"
-<param name="xtandem_min_frag_mz" type="integer" value="200"
+label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
-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_frag_mz" type="integer" value="200"
-<param name="xtandem_min_prec_mass" 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"/>
-label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+<param name="xtandem_min_prec_mass" type="integer" value="200"
-<param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
+label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+<param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
-<param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
+label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
-label="X!Tandem: Dynamic Range" value="100" type="integer" />
+<param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
-<param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
+label="X!Tandem: Dynamic Range" value="100" type="integer" />
-label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+<param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
-<param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
+label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+<param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
-<param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
+label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
-label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+<param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
-<param name="xtandem_evalue" help="Highest value for recorded peptides"
+label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
+<param name="xtandem_evalue" help="Highest value for recorded peptides"
-<param name="xtandem_output_proteins" help="Controls output of protein sequences"
+label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
-label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+<param name="xtandem_output_proteins" help="Controls output of protein sequences"
-<param name="xtandem_output_sequences" help="Controls output of sequence information"
+label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+<param name="xtandem_output_sequences" help="Controls output of sequence information"
-<param name="xtandem_output_spectra" help="Controls output of spectrum information"
+label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
-label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+<param name="xtandem_output_spectra" help="Controls output of spectrum information"
-<!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
+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="text" 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" />
-<conditional name="xtandem_refine"><!-- -xtandem_refine -->
+<param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
-<param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
-<option value="no" selected="True">Don't refine</option>
+<param name="omssa_neutron" type="float" value="1446.94"
-<option value="yes" >Use refinement</option>
+label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
-</param>
+<param name="omssa_low_intensity" type="float" value="0.0"
-<when value="no"/>
+label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
-<when value="yes">
+<param name="omssa_high_intensity" type="float" value="0.2"
-<param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
-label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
+<param name="omssa_intensity_incr" type="float" value="0.0005"
-<param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="OMSSA: Intensity Increment" help="Intensity increment" />
-label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
+<param name="omssa_single_window_wd" type="integer" value="27"
-<param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
-label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
+<param name="omssa_double_window_wd" type="integer" value="14"
-<param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
-label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
+<param name="omssa_single_window_pk" type="integer" value="2"
-<param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
-label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
+<param name="omssa_double_window_pk" type="integer" value="2"
-<param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
-label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
+<param name="omssa_min_ann_int_pks" type="integer" value="6"
-<param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
+label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
-label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
+<param name="omssa_min_annotated_peaks" type="integer" value="2"
-</when>
+label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
-</conditional>
+<param name="omssa_min_peaks" type="integer" value="4"
-</when>
+label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
-</conditional>
+<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" />
-<!-- OMSSA ADVANCED PARAMETERS -->
+<param name="omssa_max_ladders" type="integer" value="128"
-<conditional name="omssa">
+label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
-<param name="omssa_advanced" type="select" label="OMSSA Options">
+<param name="omssa_max_frag_charge" type="integer" value="2"
-<option value="yes">Advanced</option>
+label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
-<option value="no" selected="True">Default</option>
+<param name="omssa_fraction" type="float" value="0.95"
-</param>
+label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
-<when value="no" />
+<param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
-<when value="yes">
+label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
-<param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
+<param name="omssa_charge" type="select"
-<param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
+label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
-<param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
+<option value="0" >Minus</option>
-<param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+<option value="1" selected="True">Plus</option>
+</param>
-<param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="omssa_prec_per_spectrum" type="integer" value="1"
-label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
+label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
-<param name="omssa_neutron" type="float" value="1446.94"
+<param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
+label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
-<param name="omssa_low_intensity" type="float" value="0.0"
+<param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
+label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
-<param name="omssa_high_intensity" type="float" value="0.2"
+<param name="omssa_max_frag_series" type="integer" value="100"
-label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
+label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
-<param name="omssa_intensity_incr" type="float" value="0.0005"
+<param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Intensity Increment" help="Intensity increment" />
+label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
-<param name="omssa_single_window_wd" type="integer" value="27"
+<param name="omssa_consecutive_p" type="float" value="0.5"
-label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
+label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
-<param name="omssa_double_window_wd" type="integer" value="14"
+<param name="omssa_it_sequence_evalue" type="float" value="0.0"
-label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
+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_single_window_pk" type="integer" value="2"
+<param name="omssa_it_spectrum_evalue" type="float" value="0.01"
-label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
+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_double_window_pk" type="integer" value="2"
+<param name="omssa_it_replace_evalue" type="float" value="0.01"
-label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
+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_min_ann_int_pks" type="integer" value="6"
+<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
+label="OMSSA: Remove Precursor" help="Remove precursors" />
-<param name="omssa_min_annotated_peaks" type="integer" value="2"
+<param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
+label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
-<param name="omssa_min_peaks" type="integer" value="4"
+<param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
+label="OMSSA: Remove Precursor" help="Remove precursors" />
-<param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="omssa_max_evalue" type="float" value="100"
-label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
+label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
-<param name="omssa_max_ladders" type="integer" value="128"
+<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
+label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
-<param name="omssa_max_frag_charge" type="integer" value="2"
+<param name="omssa_it_replace_evalue" type="float" value="100"
-label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
+label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
-<param name="omssa_fraction" type="float" value="0.95"
+<param name="omssa_hitlist_length" type="integer" value="0"
-label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
+label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
-<param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="omssa_hitlist_charge" type="integer" value="30"
-label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
+label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
-<param name="omssa_charge" type="select"
+<param name="omssa_min_pep_length" type="integer" value="4"
-label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
+label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
-<option value="0" >Minus</option>
+<param name="omssa_max_pep_length" type="integer" value="40"
-<option value="1" selected="True">Plus</option>
+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>
-<param name="omssa_prec_per_spectrum" type="integer" value="1"
+<when value="no" />
-label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
+<when value="yes">
-<param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
+label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
-<param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="msgf_min_pep_length" type="integer" value="6"
-label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
+label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
-<param name="omssa_max_frag_series" type="integer" value="100"
+<param name="msgf_max_pep_length" type="integer" value="30"
-label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
+label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-<param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="msgf_termini" type="select" format="text"
-label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
+label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
-<param name="omssa_consecutive_p" type="float" value="0.5"
+<option value="0">0 (ie non-specific cleavage)</option>
-label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
+<option value="1">1 (ie semi-tryptic cleavage)</option>
-<param name="omssa_it_sequence_evalue" type="float" value="0.0"
+<option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
-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>
-<param name="omssa_it_spectrum_evalue" type="float" value="0.01"
+<param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
-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"
+<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)">
-label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
+<option value="0" selected="True">Low-res LCQ/LTQ</option>
-<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<option value="1" >High-res LTQ</option>
-label="OMSSA: Remove Precursor" help="Remove precursors" />
+<option value="2" >TOF</option>
-<param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
+<option value="3" >Q-Exactive</option>
-label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
+</param>
-<param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
-label="OMSSA: Remove Precursor" help="Remove precursors" />
+<option value="0" selected="True">As written in the spectrum or CID if no info</option>
-<param name="omssa_max_evalue" type="float" value="100"
+<option value="1" >CID</option>
-label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
+<option value="2" >ETD</option>
-<param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<option value="3" >HCD</option>
-label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
+</param>
-<param name="omssa_it_replace_evalue" type="float" value="100"
+<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">
-label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
+<option value="0" selected="True">Automatic</option>
-<param name="omssa_hitlist_length" type="integer" value="0"
+<option value="1" >Phosphorylation</option>
-label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
+<option value="2" >iTRAQ</option>
-<param name="omssa_hitlist_charge" type="integer" value="30"
+<option value="3" >iTRAQPhospho</option>
-label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
+<option value="4" >TMT</option>
-<param name="omssa_min_pep_length" type="integer" value="4"
+<option value="5" >Standard</option>
-label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
+</param>
-<param name="omssa_max_pep_length" type="integer" value="40"
+<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" />
-label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
+<param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
-<param name="omssa_format" label="OMSSA output format" type="select" >
+<option value="0" selected="True">output basic scores only</option>
-<option value="0" selected="True">OMX</option>
+<option value="1" >output additional features</option>
-<option value="1" >CSV</option>
+</param>
+</when>
+</conditional>
+<!-- MS-AMANDA ADVANCED PARAMETERS  -->
+<!-- Not working in tests
+<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>
+<when value="no" />
-</conditional>
+<when value="yes">
+<param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false"
-<!-- MS-GF+ ADVANCED PARAMETERS -->
+label="MS Amanda: Generate Decoys" help="generate decoys" />
-<conditional name="msgf">
+<param name="ms_amanda_max_evalue" type="float" value="100"
-<param name="msgf_advanced" type="select" label="MSGF Options">
+label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
-<option value="yes">Advanced</option>
+<param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
-<option value="no" selected="True">Default</option>
+<param name="ms_amanda_max_rank" type="integer" value="5"
-</param>
+label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
-<when value="no" />
+<param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
-<when value="yes">
+label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
-<param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
+</when>
-label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+</conditional>
-<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"/>
+<!-- TIDE ADVANCED PARAMETERS -->
-<param name="msgf_termini" type="select" format="text"
+<!-- Not working in tests
-label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
+<conditional name="tide">
-<option value="0">0 (ie non-specific cleavage)</option>
+<param name="tide_advanced" type="select" label="TIDE Options">
-<option value="1">1 (ie semi-tryptic cleavage)</option>
+<option value="yes">Advanced</option>
-<option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
+<option value="no" selected="True">Default</option>
 </param>
-<param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
+<when value="no" />
+<when value="yes">
-<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)">
+<param name="tide_num_ptms" type="integer" value="100"
-<option value="0" selected="True">Low-res LCQ/LTQ</option>
+label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
-<option value="1" >High-res LTQ</option>
+<param name="tide_num_ptms_per_type" type="integer" value="2"
-<option value="2" >TOF</option>
+label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
-<option value="3" >Q-Exactive</option>
+<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_output_folder" type="text" value="crux-output"
+label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
+<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="100000.0"
+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_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
+<param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
+<param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
+<param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
+<param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
+label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
+<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 -->
+<!-- Not working in tests
+<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>
-<param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
+<when value="no" />
-<option value="0" selected="True">As written in the spectrum or CID if no info</option>
+<when value="yes">
-<option value="1" >CID</option>
+<param name="myrimatch_min_pep_length"  type="integer" value="6"
-<option value="2" >ETD</option>
+label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
-<option value="3" >HCD</option>
+<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="0.0"
+label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
+<param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
+label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ 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: Number of PTMs" 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="ETD" >ETD</option>
+</param>
+<param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
+<option value="0">non-tryptic</option>
+<option value="1" >semi-tryptic</option>
+<option value="2"  selected="True" >fully-tryptic</option>
+</param>
+<param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="MyriMatch: 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: Xcorr Option" 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" />
+<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 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>
-<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">
+<when value="no" />
-<option value="0" selected="True">Automatic</option>
+<when value="yes">
-<option value="1" >Phosphorylation</option>
+<param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
-<option value="2" >iTRAQ</option>
+<param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
-<option value="3" >iTRAQPhospho</option>
+<param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
-<option value="4" >TMT</option>
+<param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
-<option value="5" >Standard</option>
+<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>
-<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" />
+<when value="no" />
-<param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
+<when value="yes">
-<option value="0" selected="True">output basic scores only</option>
+<!-- Spectrum Related parameters -->
-<option value="1" >output additional features</option>
+<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_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true"
+label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
+<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>
+<when value="no" />
-</conditional>
+<when value="yes">
+<param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
-<!-- MS-AMANDA ADVANCED PARAMETERS  -->
+<param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
-<!-- Not working in tests
+<param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
-<conditional name="ms_amanda">
+<param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
-<param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
+<param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
-<option value="yes">Advanced</option>
+<param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
-<option value="no" selected="True">Default</option>
+<param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
-</param>
+<param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
-<when value="no" />
+<param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
-<when value="yes">
+<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="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false"
+<param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
-label="MS Amanda: Generate Decoys" help="generate decoys" />
+<param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
-<param name="ms_amanda_max_evalue" type="float" value="100"
+<option value="0" selected="true">no deisotoping</option>
-label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
+<option value="1">precursor only</option>
-<param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
+<option value="2">precursor and candidate</option>
-<param name="ms_amanda_max_rank" type="integer" value="5"
+</param>
-label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
+<param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
-<param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
+<param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
-label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
+<param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
-</when>
+<param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
-</conditional>
+<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'."/>
-<!-- TIDE ADVANCED PARAMETERS -->
+</when>
-<!-- Not working in tests
+</conditional>
-<conditional name="tide">
-<param name="tide_advanced" type="select" label="TIDE Options">
+<conditional name="novor">
-<option value="yes">Advanced</option>
+<param name="novor_advanced" type="select" label="Novor Options">
-<option value="no" selected="True">Default</option>
+<option value="yes">Advanced</option>
-</param>
+<option value="no" selected="True">Default</option>
-<when value="no" />
-<when value="yes">
-<param name="tide_num_ptms" type="integer" value="100"
-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">
+<when value="no" />
-<option value="N" >N</option>
+<when value="yes">
-<option value="C" >C</option>
+<param name="novor_fragmentation" type="select" label="Novor fragmentation method">
-<option value="NC" selected="True">NC</option>
+<option value="HCD" selected="True">HCD</option>
-<option value="non" >none</option>
+<option value="CID">CID</option>
 </param>
-<param name="tide_decoy_seed" type="integer" value="1"
+<param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
-label="TIDE: Decoy Seed" help="Set the decoy seed"/>
+<option value="FT" selected="True">FT</option>
-<param name="tide_output_folder" type="text" value="crux-output"
+<option value="Trap" >Trap</option>
-label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
+<option value="TOF" >TOF</option>
-<param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
+</param>
-label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
+</when>
-<param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
+</conditional>
-<option value="0" >0</option>
+</section>
-<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="100000.0"
-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_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
-<param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
-<param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
-<param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
-<param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
-label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
-<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 -->
-<!-- Not working in tests
-<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="6"
-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="0.0"
-label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
-<param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
-label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ 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: Number of PTMs" 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="ETD" >ETD</option>
-</param>
-<param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
-<option value="0">non-tryptic</option>
-<option value="1" >semi-tryptic</option>
-<option value="2"  selected="True" >fully-tryptic</option>
-</param>
-<param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="MyriMatch: 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: Xcorr Option" 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" />
-<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 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_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
-<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>
 </inputs>
 <outputs>
 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
 </outputs>
 <tests>

Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 33:bce45e9e6d70 draft