Mercurial > repos > galaxyp > peptideshaker
changeset 43:7963340ab569 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
| author | galaxyp |
|---|---|
| date | Mon, 05 Mar 2018 10:09:34 -0500 |
| parents | 9e20c34298e3 |
| children | f35bb9d0c93e |
| files | macros.xml searchgui.xml |
| diffstat | 2 files changed, 157 insertions(+), 147 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Jan 23 08:48:07 2018 -0500 +++ b/macros.xml Mon Mar 05 10:09:34 2018 -0500 @@ -2,7 +2,7 @@ <xml name="stdio"> <stdio> <exit_code range="1:" level="fatal" description="Job Failed" /> - <regex match="java.*Exception" level="fatal" description="Java Exception"/> + <regex match="java.*Exception" level="fatal" description="Java Exception"/> <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/> <regex match="CompomicsError" level="fatal" description="Compomics Error"/> </stdio> @@ -17,8 +17,8 @@ -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} + -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 @@ -30,7 +30,7 @@ #silent $enzymes.append(str($digest.enzyme)) #silent $missed_cleavages.append(str($digest.missed_cleavages)) ## #silent $specificities.append(str($digest.specificity)) - #end for + #end for -enzyme "#echo ','.join($enzymes)#" -mc "#echo ','.join($missed_cleavages)#" ## -specificity "#echo ','.join($specificities)#" @@ -41,7 +41,7 @@ #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" + -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" @@ -79,7 +79,7 @@ <option value="Trypsin + CNBr">Trypsin + CNBr</option> <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="Whole Protein">Whole Protein</option> + <option value="Whole Protein">Whole Protein</option> <option value="Asp-N">Asp-N</option> <option value="Glu-C">Glu-C</option> <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> @@ -129,7 +129,7 @@ <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units" help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> <option value="1">Parts per million (ppm)</option> - <option value="0">Daltons</option> + <option value="0" selected="true">Daltons</option> </param> <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance" help="Provide error value for fragment ions, based on instrument used"/> @@ -157,7 +157,7 @@ <column name="value" index="0" /> </options> </param> - <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> <options from_file="searchgui_mods.loc"> <column name="name" index="0" />
--- a/searchgui.xml Tue Jan 23 08:48:07 2018 -0500 +++ b/searchgui.xml Mon Mar 05 10:09:34 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.2"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -75,12 +75,12 @@ -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_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} @@ -93,9 +93,9 @@ -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 + #else -xtandem_output_spectra 1 #end if @@ -105,37 +105,37 @@ -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} + -omssa_neutron ${advanced_options.omssa.omssa_neutron} + -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" + -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} + -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} + -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} + -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} + -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} + -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} + -omssa_methionine ${advanced_options.omssa.omssa_methionine} + -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} + -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} + -omssa_fraction ${advanced_options.omssa.omssa_fraction} + -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} + -omssa_charge ${advanced_options.omssa.omssa_charge} + -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum} + -omssa_forward ${advanced_options.omssa.omssa_forward} + -omssa_rewind ${advanced_options.omssa.omssa_rewind} + -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series} + -omssa_corr ${advanced_options.omssa.omssa_corr} + -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue} + -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length} + -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length} + -omssa_format ${advanced_options.omssa.omssa_format} #end if #if $advanced_options.msgf.msgf_advanced == "yes" @@ -144,23 +144,20 @@ -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_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} + -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 $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 ${advanced_options.ms_amanda.ms_amanda_max_rank} + -ms_amanda_instrument "${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 $advanced_options.myrimatch.myrimatch_advanced == "yes" -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length} @@ -177,7 +174,7 @@ -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} + -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak} #end if *# @@ -202,7 +199,7 @@ -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} #end if *# - + #* Not working in tests #if $advanced_options.tide.tide_advanced == "yes" -tide_num_ptms ${advanced_options.tide.tide_num_ptms} @@ -213,7 +210,7 @@ -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 ${advanced_options.tide.tide_output_folder} -tide_print_peptides ${advanced_options.tide.tide_print_peptides} -tide_verbosity ${advanced_options.tide.tide_verbosity} @@ -256,11 +253,11 @@ #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - + -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower} -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper} #end if @@ -279,7 +276,6 @@ #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 ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} #end if #end if @@ -320,7 +316,7 @@ ################ ## Search CLI ## ################ - (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI + (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="\$cwd/${bin_dir}" -temp_folder `pwd` -spectrum_files \$cwd @@ -447,7 +443,7 @@ <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> <option value="X!Tandem" selected="True">X!Tandem</option> - + <option value="MSGF" selected="True">MS-GF+</option> <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> @@ -456,7 +452,7 @@ <option value="Tide">Tide</option> <!-- Not working in tests --> - <option value="MyriMatch">MyriMatch</option> + <option value="MyriMatch">MyriMatch</option> <option value="MS_Amanda">MS_Amanda</option> <!-- Windows only <option value="Andromeda">Andromeda</option> @@ -475,7 +471,7 @@ <!-- General Parameters --> <expand macro="general_options"/> - + <section name="advanced_options" expanded="false" title="Andvanced Options"> <!-- Optional Advanced SearchGUI Parameters --> <conditional name="searchgui_advanced"> @@ -491,18 +487,18 @@ <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"> @@ -511,13 +507,13 @@ </param> <when value="no" /> <when value="yes"> - <param name="xtandem_npeaks" type="integer" value="50" + <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" + <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" + <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" + <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"/> @@ -526,9 +522,9 @@ <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" /> + 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" /> + label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> <param name="xtandem_evalue" help="Highest value for recorded peptides" label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" /> <param name="xtandem_output_proteins" help="Controls output of protein sequences" @@ -538,7 +534,7 @@ <param name="xtandem_output_spectra" help="Controls output of spectrum information" label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" /> <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." --> - + <conditional name="xtandem_refine"><!-- -xtandem_refine --> <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> <option value="no" selected="True">Don't refine</option> @@ -564,7 +560,7 @@ </conditional> </when> </conditional> - + <!-- OMSSA ADVANCED PARAMETERS --> <conditional name="omssa"> <param name="omssa_advanced" type="select" label="OMSSA Options"> @@ -577,83 +573,83 @@ <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - + <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> - <param name="omssa_neutron" type="float" value="1446.94" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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" + <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> @@ -661,7 +657,7 @@ </param> </when> </conditional> - + <!-- MS-GF+ ADVANCED PARAMETERS --> <conditional name="msgf"> <param name="msgf_advanced" type="select" label="MSGF Options"> @@ -674,16 +670,16 @@ 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" + <param name="msgf_max_pep_length" type="integer" value="30" label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> - <param name="msgf_termini" type="select" format="txt" + <param name="msgf_termini" type="select" format="txt" label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> <option value="0">0 (ie non-specific cleavage)</option> <option value="1">1 (ie semi-tryptic cleavage)</option> <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> </param> <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/> - + <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> <option value="0" selected="True">Low-res LCQ/LTQ</option> <option value="1" >High-res LTQ</option> @@ -711,9 +707,8 @@ </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> @@ -721,20 +716,37 @@ </param> <when value="no" /> <when value="yes"> - <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + <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" + <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select" + help="MS Amanda instrument id option. Available ion types are listed here."> + + <option value="b, y" selected="True">b, y</option> + <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option> + <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option> + <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option> + <option value="a, b, y" >a, b, y</option> + <option value="a, b, y, Imm" >a, b, y, Imm</option> + <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option> + <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option> + <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option> + <option value="b, y, INT" >b, y, INT</option> + <option value="b, y, INT, Imm" >b, y, INT, Imm</option> + <option value="a, b, y, INT" >a, b, y, INT</option> + <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option> + <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option> + <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option> + <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option> + + </param> + <param name="ms_amanda_max_rank" type="integer" value="10" label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> </when> </conditional> - --> - - + + <!-- TIDE ADVANCED PARAMETERS --> <!-- Not working in tests <conditional name="tide"> @@ -783,7 +795,7 @@ <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" @@ -841,7 +853,7 @@ </when> </conditional> --> - + <!-- MyriMatch ADVANCED PARAMETERS --> <!-- Not working in tests <conditional name="myrimatch"> @@ -872,10 +884,10 @@ <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" + <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_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" @@ -889,7 +901,7 @@ </when> </conditional> --> - + <!-- Andromeda ADVANCED PARAMETERS --> <!-- Windows only <conditional name="andromeda"> @@ -923,7 +935,7 @@ </when> </conditional> --> - + <!-- Comet ADVANCED PARAMETERS --> <conditional name="comet"> <param name="comet_advanced" type="select" label="Comet Options"> @@ -963,7 +975,7 @@ <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" /> + 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 --> @@ -993,12 +1005,12 @@ 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" + <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" /> + label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> </when> </conditional> <!-- Fragment Ions Related parameters --> @@ -1011,10 +1023,8 @@ <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)" /> + label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> </when> </conditional> </when> @@ -1052,7 +1062,7 @@ <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> @@ -1090,7 +1100,7 @@ <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="30000" /> + <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> </test> <!-- Test that search works with MSAmanda --> <test> @@ -1102,7 +1112,7 @@ <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="5000" /> + <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> </test> </tests> <help>