# HG changeset patch # User galaxyp # Date 1486435987 18000 # Node ID bce45e9e6d7004b61ff5ebb7f843195686095edd # Parent ff592231f118435fd6adc05be4b1b1b10e58987b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312 diff -r ff592231f118 -r bce45e9e6d70 macros.xml --- a/macros.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/macros.xml Mon Feb 06 21:53:07 2017 -0500 @@ -8,109 +8,159 @@ - -frag_tol "${fragment_tol}" + -frag_tol "${precursor_options.fragment_tol}" ### -frag_ppm - -prec_tol "${precursor_ion_tol}" - -prec_ppm "${precursor_ion_tol_units}" - ### -digestion - ### multiple enzymes? - -enzyme "${enzyme}" - ### -specificity - ### value per enzyme - -mc $missed_cleavages - #set $fixed_mods_str = $fixed_modifications or '' - #set $variable_mods_str = $variable_modifications or '' + -prec_tol "${precursor_options.precursor_ion_tol}" + -prec_ppm "${precursor_options.precursor_ion_tol_units}" + + -min_charge $precursor_options.min_charge + -max_charge $precursor_options.max_charge + -fi $precursor_options.forward_ion + -ri $precursor_options.reverse_ion + -min_isotope ${precursor_options.min_isotope} + -max_isotope ${precursor_options.max_isotope} + #if $protein_digest_options.digestion.cleavage == 'default': + ## -enzyme "Trysin" + -mc $protein_digest_options.digestion.missed_cleavages + #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0: + #set $enzymes = [] + #set $missed_cleavages = [] + ## #set $specificities = [] + #for $i, $digest in enumerate($protein_digest_options.digestion.digests): + #silent $enzymes.append(str($digest.enzyme)) + #silent $missed_cleavages.append(str($digest.missed_cleavages)) + ## #silent $specificities.append(str($digest.specificity)) + #end for + -enzyme "#echo ','.join($enzymes)#" + -mc "#echo ','.join($missed_cleavages)#" + ## -specificity "#echo ','.join($specificities)#" + #else: + -digestion $protein_digest_options.digestion.cleavage + #end if + + #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' + #set $variable_mods_str = $protein_modification_options.variable_modifications or '' #if $fixed_mods_str -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" #end if - -min_charge $min_charge - -max_charge $max_charge - -fi $forward_ion - -ri $reverse_ion - -min_isotope ${min_isotope} - -max_isotope ${max_isotope} 3 - 3.1.4 + 3.2.5 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +
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diff -r ff592231f118 -r bce45e9e6d70 peptide_shaker.xml --- a/peptide_shaker.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/peptide_shaker.xml Mon Feb 06 21:53:07 2017 -0500 @@ -1,4 +1,4 @@ - + Perform protein identification using various search engines based on results from SearchGUI @@ -6,7 +6,7 @@ macros.xml - peptide-shaker + peptide-shaker @@ -82,7 +82,7 @@ (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI --exec_dir="\$cwd/${bin_dir}" -in \$cwd/peptideshaker_output.zip - -output_file output.mzid + -output_file \$cwd/output.mzid #if $contact_options.contact_options_selector == "yes": -contact_first_name "$contact_options.contact_first_name" -contact_last_name "$contact_options.contact_last_name" @@ -337,7 +337,7 @@ - + @@ -358,7 +358,7 @@ - + diff -r ff592231f118 -r bce45e9e6d70 searchgui.xml --- a/searchgui.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/searchgui.xml Mon Feb 06 21:53:07 2017 -0500 @@ -1,4 +1,4 @@ - + Perform protein identification using various search engines and prepare results for input to Peptide Shaker @@ -23,7 +23,7 @@ export HOME=\$cwd; ## echo the search engines to run - echo "$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 @@ -41,7 +41,7 @@ ########################################### #### 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 && @@ -59,256 +59,256 @@ @GENERAL_PARAMETERS@ -db input_database.fasta - #if $use_gene_mapping: - $use_gene_mapping - $update_gene_mapping + #if $protein_database_options.use_gene_mapping: + $protein_database_options.use_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_min_peaks ${xtandem.xtandem_min_peaks} - -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz} - -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass} - -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr} - -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range} - -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} - -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} - -xtandem_stp_bias ${xtandem.xtandem_stp_bias} - -xtandem_evalue ${xtandem.xtandem_evalue} - -xtandem_output_proteins ${xtandem.xtandem_output_proteins} - -xtandem_output_sequences ${xtandem.xtandem_output_sequences} - -xtandem_output_spectra ${xtandem.xtandem_output_spectra} - ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path} + -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr} + -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range} + -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl} + -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro} + -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias} + -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue} + -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins} + -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences} + -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra} + ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path} - #if $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_semi ${xtandem.xtandem_refine.xtandem_refine_semi} - -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut} - -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps} - -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt} - -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot} - -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue} + -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue} #end if #else -xtandem_output_spectra 1 #end if - #if $omssa.omssa_advanced == "yes" - -omssa_hitlist_length ${omssa.hitlist_length} - -omssa_remove_prec ${omssa.remove_precursor} - -omssa_scale_prec ${omssa.scale_precursor} - -omssa_estimate_charge ${omssa.estimate_charge} - -omssa_memory ${omssa.omssa_memory} - -omssa_neutron ${omssa.omssa_neutron} - -omssa_low_intensity "${omssa.omssa_low_intensity}" - -omssa_high_intensity ${omssa.omssa_high_intensity} - -omssa_intensity_incr ${omssa.omssa_intensity_incr} - -omssa_single_window_wd ${omssa.omssa_single_window_wd} - -omssa_double_window_wd ${omssa.omssa_double_window_wd} - -omssa_single_window_pk ${omssa.omssa_single_window_pk} - -omssa_double_window_pk ${omssa.omssa_double_window_pk} - -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks} - -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks} - -omssa_min_peaks ${omssa.omssa_min_peaks} - -omssa_methionine ${omssa.omssa_methionine} - -omssa_max_ladders ${omssa.omssa_max_ladders} - -omssa_max_frag_charge ${omssa.omssa_max_frag_charge} - -omssa_fraction ${omssa.omssa_fraction} - -omssa_plus_one ${omssa.omssa_plus_one} - -omssa_charge ${omssa.omssa_charge} - -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum} - -omssa_forward ${omssa.omssa_forward} - -omssa_rewind ${omssa.omssa_rewind} - -omssa_max_frag_series ${omssa.omssa_max_frag_series} - -omssa_corr ${omssa.omssa_corr} - -omssa_consecutive_p ${omssa.omssa_consecutive_p} - -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue} - -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue} - -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue} - -omssa_max_evalue ${omssa.omssa_max_evalue} - -omssa_hitlist_charge ${omssa.omssa_hitlist_charge} - -omssa_min_pep_length ${omssa.omssa_min_pep_length} - -omssa_max_pep_length ${omssa.omssa_max_pep_length} - -omssa_format ${omssa.omssa_format} + #if $advanced_options.omssa.omssa_advanced == "yes" + -omssa_hitlist_length ${advanced_options.omssa.hitlist_length} + -omssa_remove_prec ${advanced_options.omssa.remove_precursor} + -omssa_scale_prec ${advanced_options.omssa.scale_precursor} + -omssa_estimate_charge ${advanced_options.omssa.estimate_charge} + -omssa_memory ${advanced_options.omssa.omssa_memory} + -omssa_neutron ${advanced_options.omssa.omssa_neutron} + -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" + -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} + -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} + -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} + -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} + -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} + -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} + -omssa_methionine ${advanced_options.omssa.omssa_methionine} + -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} + -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} + -omssa_fraction ${advanced_options.omssa.omssa_fraction} + -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} + -omssa_charge ${advanced_options.omssa.omssa_charge} + -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum} + -omssa_forward ${advanced_options.omssa.omssa_forward} + -omssa_rewind ${advanced_options.omssa.omssa_rewind} + -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series} + -omssa_corr ${advanced_options.omssa.omssa_corr} + -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue} + -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length} + -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length} + -omssa_format ${advanced_options.omssa.omssa_format} #end if - #if $msgf.msgf_advanced == "yes" - -msgf_decoy ${msgf.msgf_decoy} - -msgf_min_pep_length ${msgf.msgf_min_pep_length} - -msgf_max_pep_length ${msgf.msgf_max_pep_length} - -msgf_termini ${msgf.msgf_termini} - -msgf_num_ptms ${msgf.msgf_num_ptms} - -msgf_instrument ${msgf.msgf_instrument} - -msgf_fragmentation ${msgf.msgf_fragmentation} - -msgf_protocol ${msgf.msgf_protocol} - -msgf_num_matches ${msgf.msgf_num_matches} - -msgf_additional ${msgf.msgf_additional} + #if $advanced_options.msgf.msgf_advanced == "yes" + -msgf_decoy ${advanced_options.msgf.msgf_decoy} + -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length} + -msgf_termini ${advanced_options.msgf.msgf_termini} + -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms} + -msgf_instrument ${advanced_options.msgf.msgf_instrument} + -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation} + -msgf_protocol ${advanced_options.msgf.msgf_protocol} + -msgf_num_matches ${advanced_options.msgf.msgf_num_matches} + -msgf_additional ${advanced_options.msgf.msgf_additional} #end if #* Not working in tests - #if $ms_amanda.ms_amanda_advanced == "yes" - -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} - -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue} - -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} - -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} - -ms_amanda_mono ${ms_amanda.ms_amanda_mono} + #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes" + -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy} + -ms_amanda_max_evalue ${advanced_options.ms_amanda.ms_amanda_max_evalue} + -ms_amanda_instrument ${advanced_options.ms_amanda.ms_amanda_instrument} + -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank} + -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono} #end if *# #* Not working in tests - #if $myrimatch.myrimatch_advanced == "yes" - -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} - -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} - -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} - -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} - -myrimatch_num_matches ${myrimatch.myrimatch_num_matches} - -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms} - -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation} - -myrimatch_termini ${myrimatch.myrimatch_termini} - -myrimatch_plus_three ${myrimatch.myrimatch_plus_three} - -myrimatch_xcorr ${myrimatch.myrimatch_xcorr} - -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff} - -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} - -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} - -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} - -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} + #if $advanced_options.myrimatch.myrimatch_advanced == "yes" + -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length} + -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length} + -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass} + -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass} + -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches} + -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms} + -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation} + -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini} + -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three} + -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr} + -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff} + -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes} + -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier} + -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches} + -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak} #end if *# #* Not working in tests - #if $andromeda.andromeda_advanced == "yes" - -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} - -andromeda_max_comb ${andromeda.andromeda_max_comb} - -andromeda_top_peaks ${andromeda.andromeda_top_peaks} - -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} - -andromeda_incl_water ${andromeda.andromeda_incl_water} - -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia} - -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses} - -andromeda_fragment_all ${andromeda.andromeda_fragment_all} - -andromeda_emp_correction ${andromeda.andromeda_emp_correction} - -andromeda_higher_charge ${andromeda.andromeda_higher_charge} - -andromeda_equal_il ${andromeda.andromeda_equal_il} - -andromeda_frag_method ${andromeda.andromeda_frag_method} - -andromeda_max_mods ${andromeda.andromeda_max_mods} - -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} - -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} - -andromeda_max_psms ${andromeda.andromeda_max_psms} - -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode} + #if $advanced_options.andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb} + -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge} + -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il} + -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method} + -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} #end if *# #* Not working in tests - #if $tide.tide_advanced == "yes" - -tide_num_ptms ${tide.tide_num_ptms} - -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} - -tide_min_pep_length ${tide.tide_min_pep_length} - -tide_max_pep_length ${tide.tide_max_pep_length} - -tide_min_prec_mass ${tide.tide_min_prec_mass} - -tide_max_prec_mass ${tide.tide_max_prec_mass} - -tide_decoy_format ${tide.tide_decoy_format} - -tide_keep_terminals ${tide.tide_keep_terminals} + #if $advanced_options.tide.tide_advanced == "yes" + -tide_num_ptms ${advanced_options.tide.tide_num_ptms} + -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} + -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} + -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} + -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass} + -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} + -tide_decoy_format ${advanced_options.tide.tide_decoy_format} + -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} - -tide_output_folder ${tide.tide_output_folder} - -tide_print_peptides ${tide.tide_print_peptides} - -tide_verbosity ${tide.tide_verbosity} - -tide_monoisotopic ${tide.tide_monoisotopic} - -tide_clip_n_term ${tide.tide_clip_n_term} - -tide_digestion_type ${tide.tide_digestion_type} - -tide_compute_sp ${tide.tide_compute_sp} - -tide_max_psms ${tide.tide_max_psms} - -tide_compute_p ${tide.tide_compute_p} - -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz} - -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz} - -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks} - -tide_spectrum_charges ${tide.tide_spectrum_charges} - -tide_remove_prec ${tide.tide_remove_prec} - -tide_remove_prec_tol ${tide.tide_remove_prec_tol} - -tide_progress_indicator ${tide.tide_progress_indicator} - -tide_use_flanking ${tide.tide_use_flanking} - -tide_use_neutral_losses ${tide.tide_use_neutral_losses} - -tide_mz_bin_width ${tide.tide_mz_bin_width} - -tide_mz_bin_offset ${tide.tide_mz_bin_offset} - -tide_concat ${tide.tide_concat} - -tide_export_text ${tide.tide_export_text} - -tide_export_sqt ${tide.tide_export_sqt} - -tide_export_pepxml ${tide.tide_export_pepxml} - -tide_export_mzid ${tide.tide_export_mzid} - -tide_export_pin ${tide.tide_export_pin} - -tide_remove_temp ${tide.tide_remove_temp} + -tide_output_folder ${advanced_options.tide.tide_output_folder} + -tide_print_peptides ${advanced_options.tide.tide_print_peptides} + -tide_verbosity ${advanced_options.tide.tide_verbosity} + -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} + -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term} + -tide_digestion_type ${advanced_options.tide.tide_digestion_type} + -tide_compute_sp ${advanced_options.tide.tide_compute_sp} + -tide_max_psms ${advanced_options.tide.tide_max_psms} + -tide_compute_p ${advanced_options.tide.tide_compute_p} + -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} + -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} + -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} + -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} + -tide_remove_prec ${advanced_options.tide.tide_remove_prec} + -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol} + -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator} + -tide_use_flanking ${advanced_options.tide.tide_use_flanking} + -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses} + -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} + -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} + -tide_concat ${advanced_options.tide.tide_concat} + -tide_export_text ${advanced_options.tide.tide_export_text} + -tide_export_sqt ${advanced_options.tide.tide_export_sqt} + -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml} + -tide_export_mzid ${advanced_options.tide.tide_export_mzid} + -tide_export_pin ${advanced_options.tide.tide_export_pin} + -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" - -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} - -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} + #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" + -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks} + -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int} - -comet_remove_prec ${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" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - -comet_clear_mz_range_lower ${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_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower} + -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper} #end if - #if $comet.comet_search.comet_search_selector == "yes" - -comet_enzyme_type ${comet.comet_search.comet_enzyme_type} - -comet_isotope_correction ${comet.comet_search.comet_isotope_correction} - -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass} - -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass} - -comet_num_matches ${comet.comet_search.comet_num_matches} - -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge} - -comet_remove_meth ${comet.comet_search.comet_remove_meth} - -comet_batch_size ${comet.comet_search.comet_batch_size} - -comet_num_ptms ${comet.comet_search.comet_num_ptms} + #if $advanced_options.comet.comet_search.comet_search_selector == "yes" + -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type} + -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction} + -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass} + -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass} + -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches} + -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge} + -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth} + -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size} + -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms} #end if - #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" - -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset} - -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix} - -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions} + #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" + -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset} + -comet_sparse_matrix ${advanced_options.comet.comet_fragment_ions.comet_sparse_matrix} + -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} #end if #end if - #if $directtag.directtag_advanced == "yes" - -directag_tic_cutoff ${directtag.directag_tic_cutoff} - -directag_max_peak_count ${directtag.directag_max_peak_count} - -directag_intensity_classes ${directtag.directag_intensity_classes} - -directag_adjust_precursor ${directtag.directag_adjust_precursor} - -directag_min_adjustment ${directtag.directag_min_adjustment} - -directag_max_adjustment ${directtag.directag_max_adjustment} - -directag_adjustment_step ${directtag.directag_adjustment_step} - -directag_charge_states ${directtag.directag_charge_states} - #if str($directtag.directag_output_suffix).strip() != '': - -directag_output_suffix ${directtag.directag_output_suffix} + #if $advanced_options.directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff} + -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count} + -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes} + -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor} + -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment} + -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment} + -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step} + -directag_charge_states ${advanced_options.directtag.directag_charge_states} + #if str($advanced_options.directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${advanced_options.directtag.directag_output_suffix} #end if - -directag_ms_charge_state ${directtag.directag_ms_charge_state} - -directag_duplicate_spectra ${directtag.directag_duplicate_spectra} - -directag_deisotoping ${directtag.directag_deisotoping} - -directag_isotope_tolerance ${directtag.directag_isotope_tolerance} - -directag_complement_tolerance ${directtag.directag_complement_tolerance} - -directag_tag_length ${directtag.directag_tag_length} - -directag_max_var_mods ${directtag.directag_max_var_mods} - -directag_max_tag_count ${directtag.directag_max_tag_count} - -directag_intensity_weight ${directtag.directag_intensity_weight} - -directag_fidelity_weight ${directtag.directag_fidelity_weight} - -directag_complement_weight ${directtag.directag_complement_weight} + -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra} + -directag_deisotoping ${advanced_options.directtag.directag_deisotoping} + -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance} + -directag_tag_length ${advanced_options.directtag.directag_tag_length} + -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods} + -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count} + -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight} + -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight} + -directag_complement_weight ${advanced_options.directtag.directag_complement_weight} #end if - #if $novor.novor_advanced == "yes" - -novor_fragmentation ${novor.novor_fragmentation} - -novor_mass_analyzer ${novor.novor_mass_analyzer} + #if $advanced_options.novor.novor_advanced == "yes" + -novor_fragmentation ${advanced_options.novor.novor_fragmentation} + -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer} #end if 2> $temp_stderr) @@ -326,11 +326,11 @@ -threads "\${GALAXY_SLOTS:-12}" - #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' - -correct_titles "${searchgui_advanced.correct_titles}" - $searchgui_advanced.missing_titles - -mgf_splitting "${searchgui_advanced.mgf_splitting}" - -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" + #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced' + -correct_titles "${advanced_options.searchgui_advanced.correct_titles}" + $advanced_options.searchgui_advanced.missing_titles + -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}" + -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}" #end if ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created @@ -339,7 +339,7 @@ ##-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 @@ -425,648 +425,650 @@ - - - - + + + - - + - - Comet and Tide shouldn't both be selected since they use a similar algoritm. - - - - - - - - - - - - - - - - - +
+ + Comet and Tide shouldn't both be selected since they use a similar algoritm. + + + + + + + + + + + + + + + + + +
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - + + + + + + + - - - - - - + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + --> + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + +
diff -r ff592231f118 -r bce45e9e6d70 test-data/peptide_shaker_result1.zip Binary file test-data/peptide_shaker_result1.zip has changed diff -r ff592231f118 -r bce45e9e6d70 test-data/tiny_searchgui_result1.zip Binary file test-data/tiny_searchgui_result1.zip has changed diff -r ff592231f118 -r bce45e9e6d70 test-data/tiny_searchgui_result_amandaonly.zip Binary file test-data/tiny_searchgui_result_amandaonly.zip has changed