peptideshaker: searchgui.xml comparison

comparison searchgui.xml @ 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

comparison

equal deleted inserted replaced

-:9e20c34298e3
+:7963340ab569
-<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>
 <macros>
 <import>macros.xml</import>
 -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 $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
 -xtandem_refine 1
 -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 $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 $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 $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_instrument ${advanced_options.ms_amanda.ms_amanda_instrument}
+-ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
--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}
 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
 -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 $advanced_options.andromeda.andromeda_advanced == "yes"
 -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 $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 ${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}
 #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
 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
 #end if
 #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 $advanced_options.directtag.directtag_advanced == "yes"
 &&
 ################
 ## Search CLI ##
 ################
 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
 --exec_dir="\$cwd/${bin_dir}"
 -temp_folder `pwd`
 -spectrum_files \$cwd
 -output_folder \$cwd/output
 -id_params SEARCHGUI_IdentificationParameters.par
 <!-- Search Engine Selection -->
 <section name="search_engines_options" expanded="false" title="Search Engine Options">
 <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>
 <!-- Not working in tests
 -->
 <option value="Tide">Tide</option>
 <!-- Not working in tests
 -->
 <option value="MyriMatch">MyriMatch</option>
 <option value="MS_Amanda">MS_Amanda</option>
 <!-- Windows only
 <option value="Andromeda">Andromeda</option>
 -->
 <!-- New with version 3.0
 <!-- General Parameters -->
 <expand macro="general_options"/>
 <section name="advanced_options" expanded="false" title="Andvanced 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>
 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="0.01" />
 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
 <param name="xtandem_output_sequences" help="Controls output of sequence information"
 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
 <option value="no" selected="True">Don't refine</option>
 <option value="yes" >Use refinement</option>
 </param>
 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>
 <when value="yes">
 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
 <param name="omssa_neutron" type="float" value="1446.94"
 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
 <param name="omssa_low_intensity" type="float" value="0.0"
 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
 <param name="omssa_high_intensity" type="float" value="0.2"
 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
 <param name="omssa_intensity_incr" type="float" value="0.0005"
 label="OMSSA: Intensity Increment" help="Intensity increment" />
 <param name="omssa_single_window_wd" type="integer" value="27"
 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
 <param name="omssa_double_window_wd" type="integer" value="14"
 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
 <param name="omssa_single_window_pk" type="integer" value="2"
 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
 <param name="omssa_double_window_pk" type="integer" value="2"
 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
 <param name="omssa_min_ann_int_pks" type="integer" value="6"
 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
 <param name="omssa_min_annotated_peaks" type="integer" value="2"
 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
 <param name="omssa_min_peaks" type="integer" value="4"
 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
 <param name="omssa_max_ladders" type="integer" value="128"
 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
 <param name="omssa_max_frag_charge" type="integer" value="2"
 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
 <param name="omssa_fraction" type="float" value="0.95"
 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
 <param name="omssa_charge" type="select"
 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
 <option value="0" >Minus</option>
 <option value="1" selected="True">Plus</option>
 </param>
 <param name="omssa_prec_per_spectrum" type="integer" value="1"
 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
 <param name="omssa_max_frag_series" type="integer" value="100"
 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
 <param name="omssa_consecutive_p" type="float" value="0.5"
 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
 <param name="omssa_it_replace_evalue" type="float" value="0.01"
 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Remove Precursor" help="Remove precursors" />
 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Remove Precursor" help="Remove precursors" />
 <param name="omssa_max_evalue" type="float" value="100"
 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
 <param name="omssa_it_replace_evalue" type="float" value="100"
 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
 <param name="omssa_hitlist_length" type="integer" value="0"
 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
 <param name="omssa_hitlist_charge" type="integer" value="30"
 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
 <param name="omssa_min_pep_length" type="integer" value="4"
 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
 <param name="omssa_max_pep_length" type="integer" value="40"
 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
 <param name="omssa_format" label="OMSSA output format" type="select" >
 <option value="0" selected="True">OMX</option>
 <option value="1" >CSV</option>
 </param>
 </when>
 </conditional>
 <!-- MS-GF+ ADVANCED PARAMETERS -->
 <conditional name="msgf">
 <param name="msgf_advanced" type="select" label="MSGF Options">
 <option value="yes">Advanced</option>
 <option value="no" selected="True">Default</option>
 <when value="yes">
 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
 <param name="msgf_min_pep_length" type="integer" value="6"
 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
 <param name="msgf_max_pep_length" type="integer" value="30"
 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
 <param name="msgf_termini" type="select" format="txt"
 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
 <option value="0">0 (ie non-specific cleavage)</option>
 <option value="1">1 (ie semi-tryptic cleavage)</option>
 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
 </param>
 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
 <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
 <option value="0" selected="True">Low-res LCQ/LTQ</option>
 <option value="1" >High-res LTQ</option>
 <option value="2" >TOF</option>
 <option value="3" >Q-Exactive</option>
 <option value="0" selected="True">output basic scores only</option>
 <option value="1" >output additional features</option>
 </param>
 </when>
 </conditional>
 <!-- MS-AMANDA ADVANCED PARAMETERS  -->
-<!-- Not working in tests
 <conditional name="ms_amanda">
 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
 <option value="yes">Advanced</option>
 <option value="no" selected="True">Default</option>
 </param>
 <when 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"
+<param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
-label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
+help="MS Amanda instrument id option. Available ion types are listed here.">
-<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"
+<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">
 <param name="tide_advanced" type="select" label="TIDE Options">
 <option value="yes">Advanced</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">
 <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>
 <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"
 <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>
 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
 </when>
 </conditional>
 -->
 <!-- Comet ADVANCED PARAMETERS -->
 <conditional name="comet">
 <param name="comet_advanced" type="select" label="Comet Options">
 <option value="yes">Advanced</option>
 <option value="no" selected="True">Default</option>
 </when>
 </conditional>
 <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
 <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
 </when>
 </conditional>
 <!-- Search Related parameters -->
 <conditional name="comet_search">
 <param name="comet_search_selector" type="select" label="Comet: Search Related">
 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">
 </param>
 <when value="no" />
 <when value="yes">
 <param name="comet_frag_bin_offset"  type="float" value="0.4"
 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
-<param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true"
-label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
 <param name="comet_theoretical_fragment_ions"  type="integer" value="0"
 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
 </when>
 </conditional>
 </when>
 </conditional>
 <conditional name="directtag">
 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
 </when>
 </conditional>
 <conditional name="novor">
 <param name="novor_advanced" type="select" label="Novor Options">
 <option value="yes">Advanced</option>
 <option value="no" selected="True">Default</option>
 </param>
 <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="30000" />
 </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="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="5000" />
 </test>
 </tests>
 <help>
 **What it does**

Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 43:7963340ab569 draft