Mercurial > repos > galaxyp > peptideshaker
view searchgui.xml @ 29:78fad25eff17 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
| author | galaxyp |
|---|---|
| date | Fri, 10 Jun 2016 09:58:03 -0400 |
| parents | 432140bcc7fe |
| children | ad60446b1e93 |
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<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> </macros> <requirements> <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> <environment_variable name="LC_ALL" action="set_to">C</environment_variable> </requirements> <expand macro="stdio" /> <command> <![CDATA[ #from datetime import datetime #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") #set $temp_stderr = "searchgui_stderr" mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=\$cwd; ##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 -r "\${SEARCHGUI_JAR_PATH%/*}" bin; tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; #for $mgf in $peak_lists: #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" ln -s -f '${mgf}' '${input_name}'; #end for ##ln -s "${input_database}" input_database.fasta; cp "${input_database}" input_database.fasta; ########################################### #### Creating decoy database #### ########################################### #if $create_decoy: echo "Creating decoy database."; java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta && ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; #end if ##################################################### ## generate IdentificationParameters for SearchGUI ## ##################################################### (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI -out SEARCHGUI_IdentificationParameters.par @GENERAL_PARAMETERS@ -db input_database.fasta $use_gene_mapping #if $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} #if $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} #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_isotopes ${omssa.omssa_isotopes} -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} #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} -msgf_isotope_low ${msgf.msgf_isotope_low} -msgf_isotope_high ${msgf.msgf_isotope_high} #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} #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_isotope_low ${myrimatch.myrimatch_isotope_low} -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high} -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} #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} #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} -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} #end if *# #if $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} -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec} #if $comet.comet_spectrum.comet_remove_prec == "1" -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol} #end if #if $comet.comet_spectrum.comet_remove_prec == "2" -comet_remove_prec_tol ${comet.comet_spectrum.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} #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} #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} #end if #end if 2> $temp_stderr) && ################ ## Search CLI ## ################ (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output -id_params SEARCHGUI_IdentificationParameters.par -threads "\${GALAXY_SLOTS:-12}" #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' -correct_titles "${searchgui_advanced.correct_titles}" $searchgui_advanced.missing_titles -mgf_splitting "${searchgui_advanced.mgf_splitting}" -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" #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(',') #if 'X!Tandem' in $engines_list: -xtandem 1 #else -xtandem 0 #end if #if 'MyriMatch' in $engines_list: -myrimatch 1 #else -myrimatch 0 #end if #if 'MSGF' in $engines_list: -msgf 1 #else -msgf 0 #end if #if 'OMSSA' in $engines_list: -omssa 1 #else -omssa 0 #end if #if 'Comet' in $engines_list: -comet 1 #else -comet 0 #end if #if 'Tide' in $engines_list: -tide 1 #else -tide 0 #end if #if 'MS_Amanda' in $engines_list: -ms_amanda 1 #else -ms_amanda 0 #end if #if 'Andromeda' in $engines_list: -andromeda 1 #else -andromeda 0 #end if ## single zip file -output_option 0 ## mgf and database in output -output_data 1 2>> $temp_stderr) && (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) && (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); exit_code_for_galaxy=\$?; cat $temp_stderr 2>&1; (exit \$exit_code_for_galaxy) ]]> </command> <inputs> <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history"/> <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Create a concatenated target/decoy database before running PeptideShaker" help="Selecting this option will help PeptideShaker calculate FDR values" /> <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" label="gene mappings will be used and saved along with the project (UniProt databases only)" help="This should only be enabled for UniProt databaases" /> <param name="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"> <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> <!-- Not working in tests <option value="MyriMatch">MyriMatch</option> <option value="MS_Amanda">MS_Amanda</option> --> <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> <!-- Not working in tests <option value="Tide">Tide</option> --> <!-- Windows only <option value="Andromeda">Andromeda</option> --> <validator type="no_options" message="Please select at least one output file" /> </param> <!-- General Parameters --> <expand macro="general_options"/> <!-- Optional Advanced SearchGUI Parameters --> <conditional name="searchgui_advanced"> <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> <option value="basic" selected="True">Default</option> <option value="advanced">Advanced</option> </param> <when value="basic" /> <when value="advanced"> <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> <option value="0">no correction</option> <option value="1" selected="True">rename spectra</option> <option value="2">delete spectra</option> </param> <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" label="Add missing spectrum titles" help="(-missing_titles)"/> <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" help="Choose a smaller value if you are running on a machine with limited memory"/> <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" help="Choose a smaller value if you are running on a machine with limited memory"/> </when> </conditional> <!-- X!TANDEM ADVANCED PARAMETERS --> <conditional name="xtandem"> <param name="xtandem_advanced" type="select" label="X!Tandem Options"> <option value="yes">Advanced</option> <option value="no" selected="True">Default</option> </param> <when value="no" /> <when value="yes"> <param name="xtandem_npeaks" type="integer" value="50" label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> <param name="xtandem_min_peaks" type="integer" value="15" label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> <param name="xtandem_min_frag_mz" type="integer" value="200" label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> <param name="xtandem_min_prec_mass" type="integer" value="200" label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" label="X!Tandem: Noise Suppression" help="Use noise suppression"/> <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" label="X!Tandem: Dynamic Range" value="100" type="integer" /> <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_evalue" help="Highest value for recorded peptides" label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" /> <param name="xtandem_output_proteins" help="Controls output of protein sequences" label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_sequences" help="Controls output of sequence information" label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_output_spectra" help="Controls output of spectrum information" label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="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" /> <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> <!-- param name="omssa_isotopes" type="integer" value="0" label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / --> <param name="omssa_neutron" type="float" value="1446.94" label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> <param name="omssa_low_intensity" type="float" value="0.0" label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> <param name="omssa_high_intensity" type="float" value="0.2" label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> <param name="omssa_intensity_incr" type="float" value="0.0005" label="OMSSA: Intensity Increment" help="Intensity increment" /> <param name="omssa_single_window_wd" type="integer" value="27" label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" /> <param name="omssa_double_window_wd" type="integer" value="14" label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" /> <param name="omssa_single_window_pk" type="integer" value="2" label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" /> <param name="omssa_double_window_pk" type="integer" value="2" label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" /> <param name="omssa_min_ann_int_pks" type="integer" value="6" label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" /> <param name="omssa_min_annotated_peaks" type="integer" value="2" label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" /> <param name="omssa_min_peaks" type="integer" value="4" label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" /> <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" /> <param name="omssa_max_ladders" type="integer" value="128" label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" /> <param name="omssa_max_frag_charge" type="integer" value="2" label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" /> <param name="omssa_fraction" type="float" value="0.95" label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" /> <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/> <param name="omssa_charge" type="select" label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" > <option value="0" >Minus</option> <option value="1" selected="True">Plus</option> </param> <param name="omssa_prec_per_spectrum" type="integer" value="1" label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> <param name="omssa_max_frag_series" type="integer" value="100" label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> <param name="omssa_consecutive_p" type="float" value="0.5" label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> <param name="omssa_it_sequence_evalue" type="float" value="0.0" label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> <param name="omssa_it_spectrum_evalue" type="float" value="0.01" label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> <param name="omssa_it_replace_evalue" type="float" value="0.01" label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" /> <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Remove Precursor" help="Remove precursors" /> <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Remove Precursor" help="Remove precursors" /> <param name="omssa_max_evalue" type="float" value="100" label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" /> <param name="omssa_it_replace_evalue" type="float" value="100" label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" /> <param name="omssa_hitlist_length" type="integer" value="0" label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> <param name="omssa_hitlist_charge" type="integer" value="30" label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> <param name="omssa_min_pep_length" type="integer" value="4" label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> <param name="omssa_max_pep_length" type="integer" value="40" label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> <param name="omssa_format" label="OMSSA output format" type="select" > <option value="0" selected="True">OMX</option> <option value="1" >CSV</option> </param> </when> </conditional> <!-- MS-GF+ ADVANCED PARAMETERS --> <conditional name="msgf"> <param name="msgf_advanced" type="select" label="MSGF Options"> <option value="yes">Advanced</option> <option value="no" selected="True">Default</option> </param> <when value="no" /> <when value="yes"> <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> <param name="msgf_min_pep_length" type="integer" value="6" label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> <param name="msgf_max_pep_length" type="integer" value="30" label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> <param name="msgf_termini" type="select" format="text" label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> <option value="0">0 (ie non-specific cleavage)</option> <option value="1">1 (ie semi-tryptic cleavage)</option> <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> </param> <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/> <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> <option value="0" selected="True">Low-res LCQ/LTQ</option> <option value="1" >High-res LTQ</option> <option value="2" >TOF</option> <option value="3" >Q-Exactive</option> </param> <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> <option value="0" selected="True">As written in the spectrum or CID if no info</option> <option value="1" >CID</option> <option value="2" >ETD</option> <option value="3" >HCD</option> </param> <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples"> <option value="0" selected="True">Automatic</option> <option value="1" >Phosphorylation</option> <option value="2" >iTRAQ</option> <option value="3" >iTRAQPhospho</option> <option value="4" >TMT</option> <option value="5" >Standard</option> </param> <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export"> <option value="0" selected="True">output basic scores only</option> <option value="1" >output additional features</option> </param> <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" /> <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> </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 value="no" /> <when value="yes"> <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MS Amanda: Generate Decoys" help="generate decoys" /> <param name="ms_amanda_max_evalue" type="float" value="100" label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" /> <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.)." /> <param name="ms_amanda_max_rank" type="integer" value="5" label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> </when> </conditional> --> <!-- TIDE ADVANCED PARAMETERS --> <!-- Not working in tests <conditional name="tide"> <param name="tide_advanced" type="select" label="TIDE Options"> <option value="yes">Advanced</option> <option value="no" selected="True">Default</option> </param> <when value="no" /> <when value="yes"> <param name="tide_num_ptms" type="integer" value="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"> <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> <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_isotope_low" type="integer" value="-1" label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" /> <param name="myrimatch_isotope_high" type="integer" value="2" label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" /> <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" /> </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" /> <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> <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> </inputs> <outputs> <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> </outputs> <tests> <!-- Test that specifying non-default search engines works --> <test> <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> <param name="fixed_modifications" value="carbamidomethyl c"/> <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> <param name="xtandem.xtandem_advanced" value="yes"/> <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> </test> <!-- Test that search works with MSAmanda --> <test> <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> <param name="precursor_ion_tol" value="100"/> <param name="fixed_modifications" value="carbamidomethyl c"/> <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/> <param name="max_charge" value="3"/> <param name="engines" value="MS_Amanda"/> <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> </test> </tests> <help> **What it does** Runs multiple search engines on any number of MGF peak lists using the SearchGUI. Default: X! Tandem, OMSSA and MS-GF+ are executed. Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. </help> <expand macro="citations" /> </tool>