Mercurial > repos > galaxyp > peptideshaker
changeset 33:bce45e9e6d70 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
| author | galaxyp |
|---|---|
| date | Mon, 06 Feb 2017 21:53:07 -0500 |
| parents | ff592231f118 |
| children | 0ebf3d3e4c90 |
| files | macros.xml peptide_shaker.xml searchgui.xml test-data/peptide_shaker_result1.zip test-data/tiny_searchgui_result1.zip test-data/tiny_searchgui_result_amandaonly.zip |
| diffstat | 6 files changed, 979 insertions(+), 927 deletions(-) [+] |
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--- a/macros.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/macros.xml Mon Feb 06 21:53:07 2017 -0500 @@ -8,109 +8,159 @@ </stdio> </xml> <token name="@GENERAL_PARAMETERS@"> - -frag_tol "${fragment_tol}" + -frag_tol "${precursor_options.fragment_tol}" ### -frag_ppm - -prec_tol "${precursor_ion_tol}" - -prec_ppm "${precursor_ion_tol_units}" - ### -digestion - ### multiple enzymes? - -enzyme "${enzyme}" - ### -specificity - ### value per enzyme - -mc $missed_cleavages - #set $fixed_mods_str = $fixed_modifications or '' - #set $variable_mods_str = $variable_modifications or '' + -prec_tol "${precursor_options.precursor_ion_tol}" + -prec_ppm "${precursor_options.precursor_ion_tol_units}" + + -min_charge $precursor_options.min_charge + -max_charge $precursor_options.max_charge + -fi $precursor_options.forward_ion + -ri $precursor_options.reverse_ion + -min_isotope ${precursor_options.min_isotope} + -max_isotope ${precursor_options.max_isotope} + #if $protein_digest_options.digestion.cleavage == 'default': + ## -enzyme "Trysin" + -mc $protein_digest_options.digestion.missed_cleavages + #elif $protein_digest_options.digestion.cleavage == '0' and len($protein_digest_options.digestion.digests) > 0: + #set $enzymes = [] + #set $missed_cleavages = [] + ## #set $specificities = [] + #for $i, $digest in enumerate($protein_digest_options.digestion.digests): + #silent $enzymes.append(str($digest.enzyme)) + #silent $missed_cleavages.append(str($digest.missed_cleavages)) + ## #silent $specificities.append(str($digest.specificity)) + #end for + -enzyme "#echo ','.join($enzymes)#" + -mc "#echo ','.join($missed_cleavages)#" + ## -specificity "#echo ','.join($specificities)#" + #else: + -digestion $protein_digest_options.digestion.cleavage + #end if + + #set $fixed_mods_str = $protein_modification_options.fixed_modifications or '' + #set $variable_mods_str = $protein_modification_options.variable_modifications or '' #if $fixed_mods_str -fixed_mods "$fixed_mods_str" #end if #if $variable_mods_str -variable_mods "$variable_mods_str" #end if - -min_charge $min_charge - -max_charge $max_charge - -fi $forward_ion - -ri $reverse_ion - -min_isotope ${min_isotope} - -max_isotope ${max_isotope} </token> <token name="@SEARCHGUI_MAJOR_VERSION@">3</token> - <token name="@SEARCHGUI_VERSION@">3.1.4</token> + <token name="@SEARCHGUI_VERSION@">3.2.5</token> <xml name="general_options"> - <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" - help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> - <option value="1">Parts per million (ppm)</option> - <option value="2">Daltons</option> - </param> - <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" - help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> - <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" - help="Provide error value for fragment ions, based on instrument used"/> - <param name="enzyme" type="select" label="Enzyme" - help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> - <option value="Trypsin">Trypsin</option> - <option value="Arg-C">Arg-C</option> - <option value="CNBr">CNBr</option> - <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> - <option value="Formic Acid">Formic Acid</option> - <option value="Lys-C">Lys-C</option> - <option value="Lys-C, no P rule">Lys-C, no P rule</option> - <option value="Pepsin A">Pepsin A</option> - <option value="Trypsin + CNBr">Trypsin + CNBr</option> - <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> - <option value="Trypsin, no P rule">Trypsin, no P rule</option> - <option value="Whole Protein">Whole Protein</option> - <option value="Asp-N">Asp-N</option> - <option value="Glu-C">Glu-C</option> - <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> - <option value="Top-Down">Top-Down</option> - <option value="Semi-Tryptic">Semi-Tryptic</option> - <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> - <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> - <option value="Asp-N (DE)">Asp-N (DE)</option> - <option value="Glu-C (DE)">Glu-C (DE)</option> - <option value="Lys-N (K)">Lys-N (K)</option> - <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> - <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> - <option value="Semi-Glu-C">Semi-Glu-C</option> - <option value="LysargiNase">LysargiNase</option> - <option value="Semi-LysargiNase">Semi-LysargiNase</option> - <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> - <option value="Semi-Arg-C">Semi-Arg-C</option> - <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> - <option value="Arg-N">Arg-N</option> - <option value="Semi-Arg-N">Semi-Arg-N</option> - </param> - <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" - help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> - <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" - help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" - help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> - <options from_file="searchgui_mods.loc"> - <column name="name" index="0" /> - <column name="value" index="0" /> - </options> - </param> - <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> - <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> - <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> - <option value="a">a</option> - <option value="b" selected="true">b</option> - <option value="c">c</option> - </param> - <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> - <option value="x">x</option> - <option value="y" selected="true">y</option> - <option value="z">z</option> - </param> - <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> - <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> + + <section name="protein_digest_options" expanded="false" title="Protein Digestion Options"> + <conditional name="digestion"> + <param name="cleavage" type="select" label="Digestion"> + <option value="default" selected="true">Trypsin</option> + <option value="0">Select Enzymes</option> + <option value="1">Unspecific Cleavage</option> + <option value="2">Whole Protein</option> + </param> + <when value="default"> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + </when> + <when value="0"> + <repeat name="digests" min="1" title="Enzymes"> + <param name="enzyme" type="select" label="Enzyme" + help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used"> + <option value="Trypsin">Trypsin</option> + <option value="Arg-C">Arg-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option> + <option value="Formic Acid">Formic Acid</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-C, no P rule">Lys-C, no P rule</option> + <option value="Pepsin A">Pepsin A</option> + <option value="Trypsin + CNBr">Trypsin + CNBr</option> + <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option> + <option value="Trypsin, no P rule">Trypsin, no P rule</option> + <option value="Whole Protein">Whole Protein</option> + <option value="Asp-N">Asp-N</option> + <option value="Glu-C">Glu-C</option> + <option value="Asp-N + Glu-C">Asp-N + Glu-C</option> + <option value="Top-Down">Top-Down</option> + <option value="Semi-Tryptic">Semi-Tryptic</option> + <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! --> + <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option> + <option value="Asp-N (DE)">Asp-N (DE)</option> + <option value="Glu-C (DE)">Glu-C (DE)</option> + <option value="Lys-N (K)">Lys-N (K)</option> + <option value="Thermolysin, no P rule">Thermolysin, no P rule</option> + <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option> + <option value="Semi-Glu-C">Semi-Glu-C</option> + <option value="LysargiNase">LysargiNase</option> + <option value="Semi-LysargiNase">Semi-LysargiNase</option> + <option value="Trypsin + Glu-C">Trypsin + Glu-C</option> + <option value="Semi-Arg-C">Semi-Arg-C</option> + <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option> + <option value="Arg-N">Arg-N</option> + <option value="Semi-Arg-N">Semi-Arg-N</option> + </param> + <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages" + help="Allow peptides to contain up to this many missed enzyme cleavage sites."/> + <!-- + <param name="specificity" type="select" label="Specificity"> + <option value="0" selected="true">Specific at both termini</option> + <option value="1">Semi-Specific - one terminus</option> + <option value="2">Specific at the N-terminus only</option> + <option value="3">Specific at the C-terminus only</option> + </param> + --> + </repeat> + </when> + <when value="1"/> + <when value="2"/> + </conditional> + </section> + + <section name="precursor_options" expanded="false" title="Precursor Options"> + <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units" + help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions"> + <option value="1">Parts per million (ppm)</option> + <option value="2">Daltons</option> + </param> + <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance" + help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/> + <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)" + help="Provide error value for fragment ions, based on instrument used"/> + <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/> + <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/> + <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment"> + <option value="a">a</option> + <option value="b" selected="true">b</option> + <option value="c">c</option> + </param> + <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment"> + <option value="x">x</option> + <option value="y" selected="true">y</option> + <option value="z">z</option> + </param> + <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" /> + <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" /> + </section> + + <section name="protein_modification_options" expanded="false" title="Protein Modification Options"> + <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true" + help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true" + help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items"> + <options from_file="searchgui_mods.loc"> + <column name="name" index="0" /> + <column name="value" index="0" /> + </options> + </param> + </section> + </xml> <xml name="citations">
--- a/peptide_shaker.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/peptide_shaker.xml Mon Feb 06 21:53:07 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6"> +<tool id="peptide_shaker" name="Peptide Shaker" version="1.14.6"> <description> Perform protein identification using various search engines based on results from SearchGUI </description> @@ -6,7 +6,7 @@ <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="1.13.6">peptide-shaker</requirement> + <requirement type="package" version="1.14.6">peptide-shaker</requirement> </requirements> <expand macro="stdio" /> <command> @@ -82,7 +82,7 @@ (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI --exec_dir="\$cwd/${bin_dir}" -in \$cwd/peptideshaker_output.zip - -output_file output.mzid + -output_file \$cwd/output.mzid #if $contact_options.contact_options_selector == "yes": -contact_first_name "$contact_options.contact_first_name" -contact_last_name "$contact_options.contact_last_name" @@ -337,7 +337,7 @@ <param name="processing_options_selector" value="no"/> <param name="filtering_options_selector" value="no"/> <param name="outputs" value="zip,3"/> - <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="900" /> + <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> <output name="output_psm"> <assert_contents> <has_text text="cds.comp41779_c0_seq1" /> @@ -358,7 +358,7 @@ </output> <output name="output_hierarchical"> <assert_contents> - <has_text_matching expression="1.1\tcds.comp41779_c0_seq1; cds.comp41779_c0_seq2" /> + <has_text_matching expression="1.1\tcds.comp" /> </assert_contents> </output> <output name="output_psm">
--- a/searchgui.xml Wed Jan 25 15:37:43 2017 -0500 +++ b/searchgui.xml Mon Feb 06 21:53:07 2017 -0500 @@ -1,4 +1,4 @@ -<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> +<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> <description> Perform protein identification using various search engines and prepare results for input to Peptide Shaker </description> @@ -23,7 +23,7 @@ export HOME=\$cwd; ## echo the search engines to run - echo "$engines"; + echo "$search_engines_options.engines"; echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present @@ -41,7 +41,7 @@ ########################################### #### Creating decoy database #### ########################################### - #if $create_decoy: + #if $protein_database_options.create_decoy: echo "Creating decoy database."; searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy && rm input_database.fasta && @@ -59,256 +59,256 @@ @GENERAL_PARAMETERS@ -db input_database.fasta - #if $use_gene_mapping: - $use_gene_mapping - $update_gene_mapping + #if $protein_database_options.use_gene_mapping: + $protein_database_options.use_gene_mapping + $protein_database_options.update_gene_mapping #end if - #if $xtandem.xtandem_advanced == "yes" + #if $advanced_options.xtandem.xtandem_advanced == "yes" - -xtandem_npeaks ${xtandem.xtandem_npeaks} - -xtandem_min_peaks ${xtandem.xtandem_min_peaks} - -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz} - -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass} - -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr} - -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range} - -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} - -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} - -xtandem_stp_bias ${xtandem.xtandem_stp_bias} - -xtandem_evalue ${xtandem.xtandem_evalue} - -xtandem_output_proteins ${xtandem.xtandem_output_proteins} - -xtandem_output_sequences ${xtandem.xtandem_output_sequences} - -xtandem_output_spectra ${xtandem.xtandem_output_spectra} - ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path} + -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks} + -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks} + -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz} + -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass} + -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr} + -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range} + -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl} + -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro} + -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias} + -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue} + -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins} + -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences} + -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra} + ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path} - #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes" + #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes" -xtandem_refine 1 - -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc} - -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi} - -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut} - -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps} - -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt} - -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot} - -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue} + -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc} + -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi} + -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut} + -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps} + -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot} + -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue} #end if #else -xtandem_output_spectra 1 #end if - #if $omssa.omssa_advanced == "yes" - -omssa_hitlist_length ${omssa.hitlist_length} - -omssa_remove_prec ${omssa.remove_precursor} - -omssa_scale_prec ${omssa.scale_precursor} - -omssa_estimate_charge ${omssa.estimate_charge} - -omssa_memory ${omssa.omssa_memory} - -omssa_neutron ${omssa.omssa_neutron} - -omssa_low_intensity "${omssa.omssa_low_intensity}" - -omssa_high_intensity ${omssa.omssa_high_intensity} - -omssa_intensity_incr ${omssa.omssa_intensity_incr} - -omssa_single_window_wd ${omssa.omssa_single_window_wd} - -omssa_double_window_wd ${omssa.omssa_double_window_wd} - -omssa_single_window_pk ${omssa.omssa_single_window_pk} - -omssa_double_window_pk ${omssa.omssa_double_window_pk} - -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks} - -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks} - -omssa_min_peaks ${omssa.omssa_min_peaks} - -omssa_methionine ${omssa.omssa_methionine} - -omssa_max_ladders ${omssa.omssa_max_ladders} - -omssa_max_frag_charge ${omssa.omssa_max_frag_charge} - -omssa_fraction ${omssa.omssa_fraction} - -omssa_plus_one ${omssa.omssa_plus_one} - -omssa_charge ${omssa.omssa_charge} - -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum} - -omssa_forward ${omssa.omssa_forward} - -omssa_rewind ${omssa.omssa_rewind} - -omssa_max_frag_series ${omssa.omssa_max_frag_series} - -omssa_corr ${omssa.omssa_corr} - -omssa_consecutive_p ${omssa.omssa_consecutive_p} - -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue} - -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue} - -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue} - -omssa_max_evalue ${omssa.omssa_max_evalue} - -omssa_hitlist_charge ${omssa.omssa_hitlist_charge} - -omssa_min_pep_length ${omssa.omssa_min_pep_length} - -omssa_max_pep_length ${omssa.omssa_max_pep_length} - -omssa_format ${omssa.omssa_format} + #if $advanced_options.omssa.omssa_advanced == "yes" + -omssa_hitlist_length ${advanced_options.omssa.hitlist_length} + -omssa_remove_prec ${advanced_options.omssa.remove_precursor} + -omssa_scale_prec ${advanced_options.omssa.scale_precursor} + -omssa_estimate_charge ${advanced_options.omssa.estimate_charge} + -omssa_memory ${advanced_options.omssa.omssa_memory} + -omssa_neutron ${advanced_options.omssa.omssa_neutron} + -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}" + -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity} + -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr} + -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd} + -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd} + -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk} + -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk} + -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks} + -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks} + -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks} + -omssa_methionine ${advanced_options.omssa.omssa_methionine} + -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders} + -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge} + -omssa_fraction ${advanced_options.omssa.omssa_fraction} + -omssa_plus_one ${advanced_options.omssa.omssa_plus_one} + -omssa_charge ${advanced_options.omssa.omssa_charge} + -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum} + -omssa_forward ${advanced_options.omssa.omssa_forward} + -omssa_rewind ${advanced_options.omssa.omssa_rewind} + -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series} + -omssa_corr ${advanced_options.omssa.omssa_corr} + -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p} + -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue} + -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue} + -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue} + -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue} + -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge} + -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length} + -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length} + -omssa_format ${advanced_options.omssa.omssa_format} #end if - #if $msgf.msgf_advanced == "yes" - -msgf_decoy ${msgf.msgf_decoy} - -msgf_min_pep_length ${msgf.msgf_min_pep_length} - -msgf_max_pep_length ${msgf.msgf_max_pep_length} - -msgf_termini ${msgf.msgf_termini} - -msgf_num_ptms ${msgf.msgf_num_ptms} - -msgf_instrument ${msgf.msgf_instrument} - -msgf_fragmentation ${msgf.msgf_fragmentation} - -msgf_protocol ${msgf.msgf_protocol} - -msgf_num_matches ${msgf.msgf_num_matches} - -msgf_additional ${msgf.msgf_additional} + #if $advanced_options.msgf.msgf_advanced == "yes" + -msgf_decoy ${advanced_options.msgf.msgf_decoy} + -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length} + -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length} + -msgf_termini ${advanced_options.msgf.msgf_termini} + -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms} + -msgf_instrument ${advanced_options.msgf.msgf_instrument} + -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation} + -msgf_protocol ${advanced_options.msgf.msgf_protocol} + -msgf_num_matches ${advanced_options.msgf.msgf_num_matches} + -msgf_additional ${advanced_options.msgf.msgf_additional} #end if #* Not working in tests - #if $ms_amanda.ms_amanda_advanced == "yes" - -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} - -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue} - -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} - -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} - -ms_amanda_mono ${ms_amanda.ms_amanda_mono} + #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes" + -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy} + -ms_amanda_max_evalue ${advanced_options.ms_amanda.ms_amanda_max_evalue} + -ms_amanda_instrument ${advanced_options.ms_amanda.ms_amanda_instrument} + -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank} + -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono} #end if *# #* Not working in tests - #if $myrimatch.myrimatch_advanced == "yes" - -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} - -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} - -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} - -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} - -myrimatch_num_matches ${myrimatch.myrimatch_num_matches} - -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms} - -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation} - -myrimatch_termini ${myrimatch.myrimatch_termini} - -myrimatch_plus_three ${myrimatch.myrimatch_plus_three} - -myrimatch_xcorr ${myrimatch.myrimatch_xcorr} - -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff} - -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} - -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} - -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} - -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} + #if $advanced_options.myrimatch.myrimatch_advanced == "yes" + -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length} + -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length} + -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass} + -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass} + -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches} + -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms} + -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation} + -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini} + -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three} + -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr} + -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff} + -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes} + -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier} + -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches} + -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak} #end if *# #* Not working in tests - #if $andromeda.andromeda_advanced == "yes" - -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} - -andromeda_max_comb ${andromeda.andromeda_max_comb} - -andromeda_top_peaks ${andromeda.andromeda_top_peaks} - -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} - -andromeda_incl_water ${andromeda.andromeda_incl_water} - -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia} - -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses} - -andromeda_fragment_all ${andromeda.andromeda_fragment_all} - -andromeda_emp_correction ${andromeda.andromeda_emp_correction} - -andromeda_higher_charge ${andromeda.andromeda_higher_charge} - -andromeda_equal_il ${andromeda.andromeda_equal_il} - -andromeda_frag_method ${andromeda.andromeda_frag_method} - -andromeda_max_mods ${andromeda.andromeda_max_mods} - -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} - -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} - -andromeda_max_psms ${andromeda.andromeda_max_psms} - -andromeda_decoy_mode ${andromeda.andromeda_decoy_mode} + #if $advanced_options.andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb} + -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge} + -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il} + -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method} + -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms} + -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} #end if *# #* Not working in tests - #if $tide.tide_advanced == "yes" - -tide_num_ptms ${tide.tide_num_ptms} - -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} - -tide_min_pep_length ${tide.tide_min_pep_length} - -tide_max_pep_length ${tide.tide_max_pep_length} - -tide_min_prec_mass ${tide.tide_min_prec_mass} - -tide_max_prec_mass ${tide.tide_max_prec_mass} - -tide_decoy_format ${tide.tide_decoy_format} - -tide_keep_terminals ${tide.tide_keep_terminals} + #if $advanced_options.tide.tide_advanced == "yes" + -tide_num_ptms ${advanced_options.tide.tide_num_ptms} + -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} + -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} + -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} + -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass} + -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} + -tide_decoy_format ${advanced_options.tide.tide_decoy_format} + -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} - -tide_output_folder ${tide.tide_output_folder} - -tide_print_peptides ${tide.tide_print_peptides} - -tide_verbosity ${tide.tide_verbosity} - -tide_monoisotopic ${tide.tide_monoisotopic} - -tide_clip_n_term ${tide.tide_clip_n_term} - -tide_digestion_type ${tide.tide_digestion_type} - -tide_compute_sp ${tide.tide_compute_sp} - -tide_max_psms ${tide.tide_max_psms} - -tide_compute_p ${tide.tide_compute_p} - -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz} - -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz} - -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks} - -tide_spectrum_charges ${tide.tide_spectrum_charges} - -tide_remove_prec ${tide.tide_remove_prec} - -tide_remove_prec_tol ${tide.tide_remove_prec_tol} - -tide_progress_indicator ${tide.tide_progress_indicator} - -tide_use_flanking ${tide.tide_use_flanking} - -tide_use_neutral_losses ${tide.tide_use_neutral_losses} - -tide_mz_bin_width ${tide.tide_mz_bin_width} - -tide_mz_bin_offset ${tide.tide_mz_bin_offset} - -tide_concat ${tide.tide_concat} - -tide_export_text ${tide.tide_export_text} - -tide_export_sqt ${tide.tide_export_sqt} - -tide_export_pepxml ${tide.tide_export_pepxml} - -tide_export_mzid ${tide.tide_export_mzid} - -tide_export_pin ${tide.tide_export_pin} - -tide_remove_temp ${tide.tide_remove_temp} + -tide_output_folder ${advanced_options.tide.tide_output_folder} + -tide_print_peptides ${advanced_options.tide.tide_print_peptides} + -tide_verbosity ${advanced_options.tide.tide_verbosity} + -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} + -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term} + -tide_digestion_type ${advanced_options.tide.tide_digestion_type} + -tide_compute_sp ${advanced_options.tide.tide_compute_sp} + -tide_max_psms ${advanced_options.tide.tide_max_psms} + -tide_compute_p ${advanced_options.tide.tide_compute_p} + -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} + -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} + -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} + -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} + -tide_remove_prec ${advanced_options.tide.tide_remove_prec} + -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol} + -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator} + -tide_use_flanking ${advanced_options.tide.tide_use_flanking} + -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses} + -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} + -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} + -tide_concat ${advanced_options.tide.tide_concat} + -tide_export_text ${advanced_options.tide.tide_export_text} + -tide_export_sqt ${advanced_options.tide.tide_export_sqt} + -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml} + -tide_export_mzid ${advanced_options.tide.tide_export_mzid} + -tide_export_pin ${advanced_options.tide.tide_export_pin} + -tide_remove_temp ${advanced_options.tide.tide_remove_temp} #end if *# - #if $comet.comet_advanced == "yes" + #if $advanced_options.comet.comet_advanced == "yes" - #if $comet.comet_spectrum.comet_spectrum_selector == "yes" - -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} - -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int} + #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" + -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks} + -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int} - -comet_remove_prec ${comet.comet_spectrum.comet_prec.comet_remove_prec} + -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec} - #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "1" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - #if $comet.comet_spectrum.comet_prec.comet_remove_prec == "2" - -comet_remove_prec_tol ${comet.comet_spectrum.comet_prec.comet_remove_prec_tol} + #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2" + -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol} #end if - -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower} - -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper} + -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower} + -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper} #end if - #if $comet.comet_search.comet_search_selector == "yes" - -comet_enzyme_type ${comet.comet_search.comet_enzyme_type} - -comet_isotope_correction ${comet.comet_search.comet_isotope_correction} - -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass} - -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass} - -comet_num_matches ${comet.comet_search.comet_num_matches} - -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge} - -comet_remove_meth ${comet.comet_search.comet_remove_meth} - -comet_batch_size ${comet.comet_search.comet_batch_size} - -comet_num_ptms ${comet.comet_search.comet_num_ptms} + #if $advanced_options.comet.comet_search.comet_search_selector == "yes" + -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type} + -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction} + -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass} + -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass} + -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches} + -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge} + -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth} + -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size} + -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms} #end if - #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" - -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset} - -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix} - -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions} + #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes" + -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset} + -comet_sparse_matrix ${advanced_options.comet.comet_fragment_ions.comet_sparse_matrix} + -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions} #end if #end if - #if $directtag.directtag_advanced == "yes" - -directag_tic_cutoff ${directtag.directag_tic_cutoff} - -directag_max_peak_count ${directtag.directag_max_peak_count} - -directag_intensity_classes ${directtag.directag_intensity_classes} - -directag_adjust_precursor ${directtag.directag_adjust_precursor} - -directag_min_adjustment ${directtag.directag_min_adjustment} - -directag_max_adjustment ${directtag.directag_max_adjustment} - -directag_adjustment_step ${directtag.directag_adjustment_step} - -directag_charge_states ${directtag.directag_charge_states} - #if str($directtag.directag_output_suffix).strip() != '': - -directag_output_suffix ${directtag.directag_output_suffix} + #if $advanced_options.directtag.directtag_advanced == "yes" + -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff} + -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count} + -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes} + -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor} + -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment} + -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment} + -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step} + -directag_charge_states ${advanced_options.directtag.directag_charge_states} + #if str($advanced_options.directtag.directag_output_suffix).strip() != '': + -directag_output_suffix ${advanced_options.directtag.directag_output_suffix} #end if - -directag_ms_charge_state ${directtag.directag_ms_charge_state} - -directag_duplicate_spectra ${directtag.directag_duplicate_spectra} - -directag_deisotoping ${directtag.directag_deisotoping} - -directag_isotope_tolerance ${directtag.directag_isotope_tolerance} - -directag_complement_tolerance ${directtag.directag_complement_tolerance} - -directag_tag_length ${directtag.directag_tag_length} - -directag_max_var_mods ${directtag.directag_max_var_mods} - -directag_max_tag_count ${directtag.directag_max_tag_count} - -directag_intensity_weight ${directtag.directag_intensity_weight} - -directag_fidelity_weight ${directtag.directag_fidelity_weight} - -directag_complement_weight ${directtag.directag_complement_weight} + -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state} + -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra} + -directag_deisotoping ${advanced_options.directtag.directag_deisotoping} + -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance} + -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance} + -directag_tag_length ${advanced_options.directtag.directag_tag_length} + -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods} + -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count} + -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight} + -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight} + -directag_complement_weight ${advanced_options.directtag.directag_complement_weight} #end if - #if $novor.novor_advanced == "yes" - -novor_fragmentation ${novor.novor_fragmentation} - -novor_mass_analyzer ${novor.novor_mass_analyzer} + #if $advanced_options.novor.novor_advanced == "yes" + -novor_fragmentation ${advanced_options.novor.novor_fragmentation} + -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer} #end if 2> $temp_stderr) @@ -326,11 +326,11 @@ -threads "\${GALAXY_SLOTS:-12}" - #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' - -correct_titles "${searchgui_advanced.correct_titles}" - $searchgui_advanced.missing_titles - -mgf_splitting "${searchgui_advanced.mgf_splitting}" - -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" + #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced' + -correct_titles "${advanced_options.searchgui_advanced.correct_titles}" + $advanced_options.searchgui_advanced.missing_titles + -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}" + -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}" #end if ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created @@ -339,7 +339,7 @@ ##-makeblastdb_folder \$BLAST_ROOT_DIR - #set $engines_list = str($engines).split(',') + #set $engines_list = str($search_engines_options.engines).split(',') #if 'X!Tandem' in $engines_list: -xtandem 1 #else @@ -425,648 +425,650 @@ <param format="fasta" name="input_database" type="data" label="Protein Database" help="Select FASTA database from history"/> - - <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" - label="Create a concatenated target/decoy database before running PeptideShaker" - help="Selecting this option will help PeptideShaker calculate FDR values" /> - - <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" - label="gene mappings will be used and saved along with the project (UniProt databases only)" + <section name="protein_database_options" expanded="false" title="Protein Database Options"> + <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" + label="Create a concatenated target/decoy database before running PeptideShaker" + help="Selecting this option will help PeptideShaker calculate FDR values" /> + <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false" + label="gene mappings will be used and saved along with the project (UniProt databases only)" + help="This should only be enabled for UniProt databaases" /> + <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false" + label="Update gene mappings automatically from Ensembl (UniProt databases only)" help="This should only be enabled for UniProt databaases" /> - <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false" - label="Update gene mappings automatically from Ensembl (UniProt databases only)" - help="This should only be enabled for UniProt databaases" /> - + </section> <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" help="Select appropriate MGF dataset(s) from history" /> <!-- Search Engine Selection --> - <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> - <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> - <option value="X!Tandem" selected="True">X!Tandem</option> - - <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 - --> - <!--working in tests - --> - <option value="DirecTag">DirecTag</option> - <option value="Novor">Novor (Select for non-commercial use only)</option> - <validator type="no_options" message="Please select at least one output file" /> - </param> + <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 + --> + <!--working in tests + --> + <option value="DirecTag">DirecTag</option> + <option value="Novor">Novor (Select for non-commercial use only)</option> + <validator type="no_options" message="Please select at least one output file" /> + </param> + </section> <!-- General Parameters --> <expand macro="general_options"/> - <!-- Optional Advanced SearchGUI Parameters --> - <conditional name="searchgui_advanced"> - <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> - <option value="basic" selected="True">Default</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" - help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> - <option value="0">no correction</option> - <option value="1" selected="True">rename spectra</option> - <option value="2">delete spectra</option> - </param> - - <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" - label="Add missing spectrum titles" help="(-missing_titles)"/> - - <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" - help="Choose a smaller value if you are running on a machine with limited memory"/> - - <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" - help="Choose a smaller value if you are running on a machine with limited memory"/> - </when> - </conditional> - - - <!-- X!TANDEM ADVANCED PARAMETERS --> - <conditional name="xtandem"> - <param name="xtandem_advanced" type="select" label="X!Tandem Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="xtandem_npeaks" type="integer" value="50" - label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> - <param name="xtandem_min_peaks" type="integer" value="15" - label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> - <param name="xtandem_min_frag_mz" type="integer" value="200" - label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> - <param name="xtandem_min_prec_mass" type="integer" value="200" - label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> - <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" - label="X!Tandem: Noise Suppression" help="Use noise suppression"/> - <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" - label="X!Tandem: Dynamic Range" value="100" type="integer" /> - <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" - label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" - label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" - label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> - <param name="xtandem_evalue" help="Highest value for recorded peptides" - label="X!Tandem: Maximum Valid Expectation Value" type="float" value="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="text" help="Path to a spectrum data file for use by skyline." --> - - <conditional name="xtandem_refine"><!-- -xtandem_refine --> - <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> - <option value="no" selected="True">Don't refine</option> - <option value="yes" >Use refinement</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> - <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> - <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> - <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> - <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> - <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/> - <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement" - label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> - </when> - </conditional> - </when> - </conditional> - - <!-- OMSSA ADVANCED PARAMETERS --> - <conditional name="omssa"> - <param name="omssa_advanced" type="select" label="OMSSA Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> - <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> - <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> - <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> - - <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> - <param name="omssa_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> + + <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> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" + help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> + <option value="0">no correction</option> + <option value="1" selected="True">rename spectra</option> + <option value="2">delete spectra</option> + </param> + + <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" + label="Add missing spectrum titles" help="(-missing_titles)"/> + + <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" + help="Choose a smaller value if you are running on a machine with limited memory"/> + + <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" + help="Choose a smaller value if you are running on a machine with limited memory"/> + </when> + </conditional> + + <!-- X!TANDEM ADVANCED PARAMETERS --> + <conditional name="xtandem"> + <param name="xtandem_advanced" type="select" label="X!Tandem Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="xtandem_npeaks" type="integer" value="50" + label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> + <param name="xtandem_min_peaks" type="integer" value="15" + label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> + <param name="xtandem_min_frag_mz" type="integer" value="200" + label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> + <param name="xtandem_min_prec_mass" type="integer" value="200" + label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> + <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" + label="X!Tandem: Noise Suppression" help="Use noise suppression"/> + <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra" + label="X!Tandem: Dynamic Range" value="100" type="integer" /> + <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection" + label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection" + label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models" + label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> + <param name="xtandem_evalue" help="Highest value for recorded peptides" + label="X!Tandem: Maximum Valid Expectation Value" type="float" value="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="text" help="Path to a spectrum data file for use by skyline." --> + + <conditional name="xtandem_refine"><!-- -xtandem_refine --> + <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> + <option value="no" selected="True">Don't refine</option> + <option value="yes" >Use refinement</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> + <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> + <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/> + <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/> + <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/> + <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/> + <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement" + label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" /> + </when> + </conditional> + </when> + </conditional> + + <!-- OMSSA ADVANCED PARAMETERS --> + <conditional name="omssa"> + <param name="omssa_advanced" type="select" label="OMSSA Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> </param> - <param name="omssa_prec_per_spectrum" type="integer" value="1" - label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> - <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> - <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> - <param name="omssa_max_frag_series" type="integer" value="100" - label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> - <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> - <param name="omssa_consecutive_p" type="float" value="0.5" - label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> - <param name="omssa_it_sequence_evalue" type="float" value="0.0" - label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> - <param name="omssa_it_spectrum_evalue" type="float" value="0.01" - label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> - <param name="omssa_it_replace_evalue" type="float" value="0.01" - label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" /> - <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Remove Precursor" help="Remove precursors" /> - <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> - <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Remove Precursor" help="Remove precursors" /> - <param name="omssa_max_evalue" type="float" value="100" - label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> - <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" /> - <param name="omssa_it_replace_evalue" type="float" value="100" - label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" /> - <param name="omssa_hitlist_length" type="integer" value="0" - label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> - <param name="omssa_hitlist_charge" type="integer" value="30" - label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> - <param name="omssa_min_pep_length" type="integer" value="4" - label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> - <param name="omssa_max_pep_length" type="integer" value="40" - label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> - <param name="omssa_format" label="OMSSA output format" type="select" > - <option value="0" selected="True">OMX</option> - <option value="1" >CSV</option> - </param> - </when> - </conditional> - - <!-- MS-GF+ ADVANCED PARAMETERS --> - <conditional name="msgf"> - <param name="msgf_advanced" type="select" label="MSGF Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> - <param name="msgf_min_pep_length" type="integer" value="6" - label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> - <param name="msgf_max_pep_length" type="integer" value="30" - label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> - <param name="msgf_termini" type="select" format="text" - label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> - <option value="0">0 (ie non-specific cleavage)</option> - <option value="1">1 (ie semi-tryptic cleavage)</option> - <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> - </param> - <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/> - - <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> - <option value="0" selected="True">Low-res LCQ/LTQ</option> - <option value="1" >High-res LTQ</option> - <option value="2" >TOF</option> - <option value="3" >Q-Exactive</option> + <when value="no" /> + <when value="yes"> + <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> + <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> + <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> + <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> + + <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> + <param name="omssa_neutron" type="float" value="1446.94" + label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> + <param name="omssa_low_intensity" type="float" value="0.0" + label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> + <param name="omssa_high_intensity" type="float" value="0.2" + label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> + <param name="omssa_intensity_incr" type="float" value="0.0005" + label="OMSSA: Intensity Increment" help="Intensity increment" /> + <param name="omssa_single_window_wd" type="integer" value="27" + label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" /> + <param name="omssa_double_window_wd" type="integer" value="14" + label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" /> + <param name="omssa_single_window_pk" type="integer" value="2" + label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" /> + <param name="omssa_double_window_pk" type="integer" value="2" + label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" /> + <param name="omssa_min_ann_int_pks" type="integer" value="6" + label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" /> + <param name="omssa_min_annotated_peaks" type="integer" value="2" + label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" /> + <param name="omssa_min_peaks" type="integer" value="4" + label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" /> + <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" /> + <param name="omssa_max_ladders" type="integer" value="128" + label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" /> + <param name="omssa_max_frag_charge" type="integer" value="2" + label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" /> + <param name="omssa_fraction" type="float" value="0.95" + label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" /> + <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/> + <param name="omssa_charge" type="select" + label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" > + <option value="0" >Minus</option> + <option value="1" selected="True">Plus</option> + </param> + <param name="omssa_prec_per_spectrum" type="integer" value="1" + label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" /> + <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" /> + <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" /> + <param name="omssa_max_frag_series" type="integer" value="100" + label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" /> + <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" /> + <param name="omssa_consecutive_p" type="float" value="0.5" + label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" /> + <param name="omssa_it_sequence_evalue" type="float" value="0.0" + label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" /> + <param name="omssa_it_spectrum_evalue" type="float" value="0.01" + label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" /> + <param name="omssa_it_replace_evalue" type="float" value="0.01" + label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="OMSSA: Scale Precursor Mass" help="scale precursor mass" /> + <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Remove Precursor" help="Remove precursors" /> + <param name="omssa_max_evalue" type="float" value="100" + label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" /> + <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" /> + <param name="omssa_it_replace_evalue" type="float" value="100" + label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" /> + <param name="omssa_hitlist_length" type="integer" value="0" + label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" /> + <param name="omssa_hitlist_charge" type="integer" value="30" + label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" /> + <param name="omssa_min_pep_length" type="integer" value="4" + label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" /> + <param name="omssa_max_pep_length" type="integer" value="40" + label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" /> + <param name="omssa_format" label="OMSSA output format" type="select" > + <option value="0" selected="True">OMX</option> + <option value="1" >CSV</option> + </param> + </when> + </conditional> + + <!-- MS-GF+ ADVANCED PARAMETERS --> + <conditional name="msgf"> + <param name="msgf_advanced" type="select" label="MSGF Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> </param> - <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> + <when value="no" /> + <when value="yes"> + <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/> + <param name="msgf_min_pep_length" type="integer" value="6" + label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> + <param name="msgf_max_pep_length" type="integer" value="30" + label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> + <param name="msgf_termini" type="select" format="text" + label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> + <option value="0">0 (ie non-specific cleavage)</option> + <option value="1">1 (ie semi-tryptic cleavage)</option> + <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option> + </param> + <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/> + + <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)"> + <option value="0" selected="True">Low-res LCQ/LTQ</option> + <option value="1" >High-res LTQ</option> + <option value="2" >TOF</option> + <option value="3" >Q-Exactive</option> + </param> + <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)"> + <option value="0" selected="True">As written in the spectrum or CID if no info</option> + <option value="1" >CID</option> + <option value="2" >ETD</option> + <option value="3" >HCD</option> + </param> + <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples"> + <option value="0" selected="True">Automatic</option> + <option value="1" >Phosphorylation</option> + <option value="2" >iTRAQ</option> + <option value="3" >iTRAQPhospho</option> + <option value="4" >TMT</option> + <option value="5" >Standard</option> + </param> + <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> + <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export"> + <option value="0" selected="True">output basic scores only</option> + <option value="1" >output additional features</option> + </param> + </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> - </conditional> - - <!-- MS-AMANDA ADVANCED PARAMETERS --> - <!-- Not working in tests - <conditional name="ms_amanda"> - <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="MS Amanda: Generate Decoys" help="generate decoys" /> - <param name="ms_amanda_max_evalue" type="float" value="100" - label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" /> - <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." /> - <param name="ms_amanda_max_rank" type="integer" value="5" - label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> - <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> - </when> - </conditional> - --> - - - <!-- TIDE ADVANCED PARAMETERS --> - <!-- Not working in tests - <conditional name="tide"> - <param name="tide_advanced" type="select" label="TIDE Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="tide_num_ptms" type="integer" value="100" - label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> - <param name="tide_num_ptms_per_type" type="integer" value="2" - label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> - <param name="tide_min_pep_length" type="integer" value="6" - label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> - <param name="tide_max_pep_length" type="integer" value="30" - label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/> - <param name="tide_min_prec_mass" type="float" value="200.0" - label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/> - <param name="tide_max_prec_mass" type="float" value="7200.0" - label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/> - <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences"> - <option value="none" selected="True">none</option> - <option value="shuffle" >shuffle</option> - <option value="peptide-revers" >peptide-reverse</option> - <option value="protein-reverse" >protein-reverse</option> - </param> - <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys"> - <option value="N" >N</option> - <option value="C" >C</option> - <option value="NC" selected="True">NC</option> - <option value="non" >none</option> + <when value="no" /> + <when value="yes"> + <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MS Amanda: Generate Decoys" help="generate decoys" /> + <param name="ms_amanda_max_evalue" type="float" value="100" + label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" /> + <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." /> + <param name="ms_amanda_max_rank" type="integer" value="5" + label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> + <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> + </when> + </conditional> + --> + + + <!-- TIDE ADVANCED PARAMETERS --> + <!-- Not working in tests + <conditional name="tide"> + <param name="tide_advanced" type="select" label="TIDE Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> </param> - <param name="tide_decoy_seed" type="integer" value="1" - label="TIDE: Decoy Seed" help="Set the decoy seed"/> - <param name="tide_output_folder" type="text" value="crux-output" - label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/> - <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> - <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> - <option value="0" >0</option> - <option value="10" >10</option> - <option value="20" >20</option> - <option value="30" selected="True">30</option> - <option value="40" >40</option> - <option value="50" >50</option> - <option value="60" >60</option> - </param> - - <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/> - <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/> - <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules"> - <option value="full-digest" selected="True">full-digest</option> - <option value="partial-digest" >partial-digest</option> - </param> - <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Compute SP" help="If true, the SP-score is calculated"/> - <param name="tide_max_psms" type="integer" value="10" - label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> - <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> - <param name="tide_min_spectrum_mz" type="float" value="0.0" - label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> - <param name="tide_max_spectrum_mz" type="float" value="100000.0" - label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> - <param name="tide_min_spectrum_peaks" type="integer" value="20" - label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> - <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> - <option value="1" >1</option> - <option value="2" >2</option> - <option value="3" >3</option> - <option value="all" selected="True">all</option> + <when value="no" /> + <when value="yes"> + <param name="tide_num_ptms" type="integer" value="100" + label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> + <param name="tide_num_ptms_per_type" type="integer" value="2" + label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> + <param name="tide_min_pep_length" type="integer" value="6" + label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> + <param name="tide_max_pep_length" type="integer" value="30" + label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/> + <param name="tide_min_prec_mass" type="float" value="200.0" + label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/> + <param name="tide_max_prec_mass" type="float" value="7200.0" + label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/> + <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences"> + <option value="none" selected="True">none</option> + <option value="shuffle" >shuffle</option> + <option value="peptide-revers" >peptide-reverse</option> + <option value="protein-reverse" >protein-reverse</option> + </param> + <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys"> + <option value="N" >N</option> + <option value="C" >C</option> + <option value="NC" selected="True">NC</option> + <option value="non" >none</option> + </param> + <param name="tide_decoy_seed" type="integer" value="1" + label="TIDE: Decoy Seed" help="Set the decoy seed"/> + <param name="tide_output_folder" type="text" value="crux-output" + label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/> + <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> + <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> + <option value="0" >0</option> + <option value="10" >10</option> + <option value="20" >20</option> + <option value="30" selected="True">30</option> + <option value="40" >40</option> + <option value="50" >50</option> + <option value="60" >60</option> + </param> + + <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/> + <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/> + <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules"> + <option value="full-digest" selected="True">full-digest</option> + <option value="partial-digest" >partial-digest</option> + </param> + <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute SP" help="If true, the SP-score is calculated"/> + <param name="tide_max_psms" type="integer" value="10" + label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> + <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> + <param name="tide_min_spectrum_mz" type="float" value="0.0" + label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_max_spectrum_mz" type="float" value="100000.0" + label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> + <param name="tide_min_spectrum_peaks" type="integer" value="20" + label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> + <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> + <option value="1" >1</option> + <option value="2" >2</option> + <option value="3" >3</option> + <option value="all" selected="True">all</option> + </param> + <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/> + <param name="tide_remove_prec_tol" type="float" value="1.5" + label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/> + <param name="tide_progress_indicator" type="integer" value="1000" + label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/> + <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/> + <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/> + <param name="tide_mz_bin_width" type="float" value="0.02" + label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> + <param name="tide_mz_bin_offset" type="float" value="0.0" + label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> + <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> + <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/> + <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/> + <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/> + <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/> + <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> + <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> + </when> + </conditional> + --> + + <!-- MyriMatch ADVANCED PARAMETERS --> + <!-- Not working in tests + <conditional name="myrimatch"> + <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> </param> - <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/> - <param name="tide_remove_prec_tol" type="float" value="1.5" - label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/> - <param name="tide_progress_indicator" type="integer" value="1000" - label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/> - <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/> - <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/> - <param name="tide_mz_bin_width" type="float" value="0.02" - label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> - <param name="tide_mz_bin_offset" type="float" value="0.0" - label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> - <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> - <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/> - <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/> - <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/> - <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/> - <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> - <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> - </when> - </conditional> - --> - - <!-- MyriMatch ADVANCED PARAMETERS --> - <!-- Not working in tests - <conditional name="myrimatch"> - <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="myrimatch_min_pep_length" type="integer" value="6" - label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" /> - <param name="myrimatch_max_pep_length" type="integer" value="30" - label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> - <param name="myrimatch_min_prec_mass" type="float" value="0.0" - label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" /> - <param name="myrimatch_max_prec_mass" type="float" value="10000.0" - label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" /> - <param name="myrimatch_num_matches" type="integer" value="10" - label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> - <param name="myrimatch_num_ptms" type="integer" value="2" - label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" /> - <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> - <option value="CID" selected="True">CID</option> - <option value="ETD" >ETD</option> - </param> - <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini"> - <option value="0">non-tryptic</option> - <option value="1" >semi-tryptic</option> - <option value="2" selected="True" >fully-tryptic</option> - </param> - <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> - <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" - label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> - <param name="myrimatch_tic_cutoff" type="float" value="0.98" - label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" /> - <param name="myrimatch_intensity_classes" type="integer" value="3" - label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> - <param name="myrimatch_class_multiplier" type="integer" value="2" - label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> - <param name="myrimatch_num_batches" type="integer" value="50" - label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> - <param name="myrimatch_max_peak" type="integer" value="100" - label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> - </when> - </conditional> - --> - - <!-- Andromeda ADVANCED PARAMETERS --> - <!-- Windows only - <conditional name="andromeda"> - <param name="andromeda_advanced" type="select" label="Andromeda Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> - <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> - <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> - <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> - <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> - <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> - <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> - <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> - <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> - <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> - <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> - <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > - <option value="CID" selected="true">CID</option> - <option value="HCD">HCD</option> - <option value="EDT">EDT</option> + <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_num_matches" type="integer" value="10" + label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> + <param name="myrimatch_num_ptms" type="integer" value="2" + label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" /> + <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> + <option value="CID" selected="True">CID</option> + <option value="ETD" >ETD</option> + </param> + <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini"> + <option value="0">non-tryptic</option> + <option value="1" >semi-tryptic</option> + <option value="2" selected="True" >fully-tryptic</option> + </param> + <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> + <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> + <param name="myrimatch_tic_cutoff" type="float" value="0.98" + label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" /> + <param name="myrimatch_intensity_classes" type="integer" value="3" + label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> + <param name="myrimatch_class_multiplier" type="integer" value="2" + label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> + <param name="myrimatch_num_batches" type="integer" value="50" + label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> + <param name="myrimatch_max_peak" type="integer" value="100" + label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> + </when> + </conditional> + --> + + <!-- Andromeda ADVANCED PARAMETERS --> + <!-- Windows only + <conditional name="andromeda"> + <param name="andromeda_advanced" type="select" label="Andromeda Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> </param> - <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> - <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> - <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> - <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> - <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> - </param> - <when value="no" /> - <when value="yes"> - <!-- Spectrum Related parameters --> - <conditional name="comet_spectrum"> - <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related"> - <option value="yes">Set Spectrum Parameters</option> - <option value="no" selected="True">Keep Default Spectrum Parameters</option> + <when value="no" /> + <when value="yes"> + <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> + <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> + <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> + <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> + <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> + <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> + <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> + <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> + <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> + <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> + <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> + <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > + <option value="CID" selected="true">CID</option> + <option value="HCD">HCD</option> + <option value="EDT">EDT</option> </param> - <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" /> - <conditional name="comet_prec"> - <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> - </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"> - <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 name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> + <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> + <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> + <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + <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> + </param> + <when value="no" /> + <when value="yes"> + <!-- Spectrum Related parameters --> + <conditional name="comet_spectrum"> + <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related"> + <option value="yes">Set Spectrum Parameters</option> + <option value="no" selected="True">Keep Default Spectrum Parameters</option> </param> - <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> + <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" /> + <conditional name="comet_prec"> + <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> + </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"> + <option value="yes">Set Search Parameters</option> + <option value="no" selected="True">Keep Default Search Parameters</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> + <when value="no" /> + <when value="yes"> + <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have"> + <option value="1">semi-specific</option> + <option value="2" selected="True">full-enzyme</option> + <option value="8">unspecific N-term</option> + <option value="9">unspecific C-term</option> + </param> + <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement"> + <option value="0" selected="True">off</option> + <option value="1">-1,0,+1,+2,+3</option> + <option value="2">-8,-4,0,+4,+8</option> + </param> + <param name="comet_min_prec_mass" type="float" value="0.0" + label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" /> + <param name="comet_max_prec_mass" type="float" value="10000.0" + label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" /> + <param name="comet_num_matches" type="integer" value="10" + label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" /> + <param name="comet_max_frag_charge" type="integer" value="3" + label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" /> + <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false" + label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" /> + <param name="comet_batch_size" type="integer" value="0" + label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" /> + <param name="comet_num_ptms" type="integer" value="10" + label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" /> + </when> + </conditional> + <!-- Fragment Ions Related parameters --> + <conditional name="comet_fragment_ions"> + <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related"> + <option value="yes">Set Fragment Ions Parameters</option> + <option value="no" selected="True">Keep Default Fragment Ions Parameters</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="comet_frag_bin_offset" type="float" value="0.4" + label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> + <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" + label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" /> + <param name="comet_theoretical_fragment_ions" type="integer" value="0" + label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> + </when> + </conditional> + </when> + </conditional> + <conditional name="directtag"> + <param name="directtag_advanced" type="select" label="DirectTag Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/> + <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/> + <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/> + <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/> + <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/> + <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/> + <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/> + <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/> + <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/> + <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/> + <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/> + <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping"> + <option value="0" selected="true">no deisotoping</option> + <option value="1">precursor only</option> + <option value="2">precursor and candidate</option> </param> - <when value="no" /> - <when value="yes"> - <param name="comet_frag_bin_offset" type="float" value="0.4" - label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" /> - <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" - label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" /> - <param name="comet_theoretical_fragment_ions" type="integer" value="0" - label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" /> - </when> - </conditional> - </when> - </conditional> - <conditional name="directtag"> - <param name="directtag_advanced" type="select" label="DirectTag Options"> - <option value="yes">Advanced</option> - <option value="no" selected="True">Default</option> - </param> - <when value="no" /> - <when value="yes"> - <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/> - <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/> - <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/> - <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/> - <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/> - <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/> - <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/> - <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/> - <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/> - <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/> - <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/> - <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping"> - <option value="0" selected="true">no deisotoping</option> - <option value="1">precursor only</option> - <option value="2">precursor and candidate</option> + <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/> + <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/> + <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/> + <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/> + <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/> + <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="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/> - <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/> - <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/> - <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/> - <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/> - <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> - <when value="no" /> - <when value="yes"> - <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> - <option value="HCD" selected="True">HCD</option> - <option value="CID">CID</option> - </param> - <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> - <option value="FT" selected="True">FT</option> - <option value="Trap" >Trap</option> - <option value="TOF" >TOF</option> - </param> - </when> - </conditional> - + <when value="no" /> + <when value="yes"> + <param name="novor_fragmentation" type="select" label="Novor fragmentation method"> + <option value="HCD" selected="True">HCD</option> + <option value="CID">CID</option> + </param> + <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra"> + <option value="FT" selected="True">FT</option> + <option value="Trap" >Trap</option> + <option value="TOF" >TOF</option> + </param> + </when> + </conditional> + </section> </inputs> <outputs> <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />