Mercurial > repos > galaxyp > peptideshaker
changeset 6:53bdfaed924d draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
| author | iracooke |
|---|---|
| date | Thu, 04 Jun 2015 08:10:26 -0400 |
| parents | cd5298908bc1 |
| children | 4a3b6a828119 |
| files | peptide_shaker.xml searchgui.xml test-data/tiny_searchgui_result1.zip |
| diffstat | 3 files changed, 406 insertions(+), 413 deletions(-) [+] |
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--- a/peptide_shaker.xml Wed Jun 03 19:38:54 2015 -0400 +++ b/peptide_shaker.xml Thu Jun 04 08:10:26 2015 -0400 @@ -161,7 +161,7 @@ ]]> </command> <inputs> - <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results" + <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" help="SearchGUI Results from History"/> <conditional name="species_type"> @@ -545,7 +545,7 @@ </outputs> <tests> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> @@ -555,7 +555,7 @@ <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="no_species_type"/> <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="yes"/> @@ -571,7 +571,7 @@ <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> </test> <test> - <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/> + <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> <param name="species_type_selector" value="Vertebrates"/> <param name="species" value="Human (Homo sapiens)"/> <param name="processing_options_selector" value="no"/>
--- a/searchgui.xml Wed Jun 03 19:38:54 2015 -0400 +++ b/searchgui.xml Thu Jun 04 08:10:26 2015 -0400 @@ -57,13 +57,13 @@ -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr} -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range} -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} - -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} - -xtandem_stp_bias ${xtandem.xtandem_stp_bias} - -xtandem_evalue ${xtandem.xtandem_evalue} - -xtandem_output_proteins ${xtandem.xtandem_output_proteins} - -xtandem_output_sequences ${xtandem.xtandem_output_sequences} - -xtandem_output_spectra ${xtandem.xtandem_output_spectra} - ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path} + -xtandem_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 @@ -74,7 +74,7 @@ -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 #end if @@ -85,38 +85,38 @@ -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} + -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" @@ -126,20 +126,20 @@ -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} + -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 - + #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} + -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 #if $myrimatch.myrimatch_advanced == "yes" @@ -159,7 +159,7 @@ -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} + -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} #end if #if $tide.tide_advanced == "yes" @@ -201,47 +201,44 @@ -tide_remove_temp ${tide.tide_remove_temp} #end if + #if $comet.comet_advanced == "yes" - #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} + #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 - + -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} - + -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 + #end if 2> $temp_stderr) && @@ -257,12 +254,12 @@ -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 + #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 @@ -270,38 +267,38 @@ ##-makeblastdb_folder \$BLAST_ROOT_DIR - #set $engines_list = str($engines).split(',') - #if 'X!Tandem' in $engines_list: + #set $engines_list = str($engines).split(',') + #if 'X!Tandem' in $engines_list: -xtandem 1 #else -xtandem 0 #end if - #if 'MyriMatch' in $engines_list: + #if 'MyriMatch' in $engines_list: -myrimatch 1 #else -myrimatch 0 #end if - #if 'MSGF' in $engines_list: + #if 'MSGF' in $engines_list: -msgf 1 #else -msgf 0 #end if - #if 'OMSSA' in $engines_list: + #if 'OMSSA' in $engines_list: -omssa 1 #else -omssa 0 #end if - #if 'Comet' in $engines_list: + #if 'Comet' in $engines_list: -comet 1 #else -comet 0 #end if - #if 'Tide' in $engines_list: + #if 'Tide' in $engines_list: -tide 1 #else -tide 0 @@ -344,7 +341,7 @@ <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 --> + <!-- Search Engine Selection --> <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> <option value="X!Tandem" selected="True">X!Tandem</option> <option value="MyriMatch">MyriMatch</option> @@ -357,11 +354,10 @@ </param> - - <!-- General Parameters --> + <!-- General Parameters --> <expand macro="general_options"/> - <!-- Optional Advanced SearchGUI Parameters --> + <!-- 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> @@ -369,26 +365,26 @@ </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="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="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_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"/> + <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 --> + + <!-- X!TANDEM ADVANCED PARAMETERS --> <conditional name="xtandem"> <param name="xtandem_advanced" type="select" label="X!Tandem Options"> <option value="yes">Advanced</option> @@ -396,7 +392,7 @@ </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" label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> @@ -406,24 +402,24 @@ 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="false" /> - <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> - + <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="false" /> + <!-- <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> @@ -444,13 +440,13 @@ <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" /> + label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> </when> </conditional> </when> </conditional> - - <!-- OMSSA ADVANCED PARAMETERS --> + + <!-- OMSSA ADVANCED PARAMETERS --> <conditional name="omssa"> <param name="omssa_advanced" type="select" label="OMSSA Options"> <option value="yes">Advanced</option> @@ -464,93 +460,92 @@ <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> - + 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 --> + <!-- MS-GF+ ADVANCED PARAMETERS --> <conditional name="msgf"> <param name="msgf_advanced" type="select" label="MSGF Options"> <option value="yes">Advanced</option> @@ -572,37 +567,37 @@ </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" /> + <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 --> + <!-- MS-AMANDA ADVANCED PARAMETERS --> <conditional name="ms_amanda"> <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> <option value="yes">Advanced</option> @@ -610,20 +605,20 @@ </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" /> + <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 --> + <!-- TIDE ADVANCED PARAMETERS --> <conditional name="tide"> <param name="tide_advanced" type="select" label="TIDE Options"> <option value="yes">Advanced</option> @@ -643,42 +638,42 @@ 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_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_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_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" @@ -691,12 +686,12 @@ 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_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" @@ -728,7 +723,7 @@ </when> </conditional> - <!-- MyriMatch ADVANCED PARAMETERS --> + <!-- MyriMatch ADVANCED PARAMETERS --> <conditional name="myrimatch"> <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> <option value="yes">Advanced</option> @@ -736,49 +731,49 @@ </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" /> + <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> - - <!-- Comet ADVANCED PARAMETERS --> + + <!-- Comet ADVANCED PARAMETERS --> <conditional name="comet"> <param name="comet_advanced" type="select" label="Comet Options"> <option value="yes">Advanced</option> @@ -786,95 +781,94 @@ </param> <when value="no" /> <when value="yes"> - <!-- Spectrum Related parameters --> - <conditional name="comet_spectrum"> + <!-- 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_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_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> - + <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> </inputs> <outputs> - <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> + <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> @@ -902,9 +896,8 @@ **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. - +Default: X! Tandem, OMSSA and MS-GF+ are executed. +Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. </help> <expand macro="citations" />