Mercurial > repos > galaxyp > fragpipe
diff msfragger_macros.xml @ 7:b4f6df8fa89b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
| author | galaxyp |
|---|---|
| date | Wed, 01 Oct 2025 22:20:54 +0000 |
| parents | 59fec1e2a6c3 |
| children |
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--- a/msfragger_macros.xml Sun Mar 30 23:00:45 2025 +0000 +++ b/msfragger_macros.xml Wed Oct 01 22:20:54 2025 +0000 @@ -38,7 +38,7 @@ <xml name="msfragger_default"> <expand macro="search_tolerances"/> <expand macro="digestion"/> - <expand macro="variable_modification"/> + <expand macro="variable_modification" mod_3="true"/> <expand macro="static_modification"/> <expand macro="glyco_labile"/> <expand macro="mass_offsets"/> @@ -50,7 +50,7 @@ <xml name="msfragger_open"> <expand macro="search_tolerances"/> <expand macro="digestion"/> - <expand macro="variable_modification"/> + <expand macro="variable_modification" mod_3="true"/> <expand macro="static_modification"/> <expand macro="glyco_labile"/> <expand macro="mass_offsets"/> @@ -62,8 +62,8 @@ <xml name="msfragger_nonspecific_HLA"> <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/> <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/> - <expand macro="variable_modification"/> - <expand macro="static_modification"/> + <expand macro="variable_modification" mod_2="true" mod_group_hla="true"/> + <expand macro="static_modification" check_cysteine="false"/> <expand macro="glyco_labile"/> <expand macro="mass_offsets"/> <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/> @@ -74,7 +74,7 @@ <xml name="msfragger_LFQ_MBR"> <expand macro="search_tolerances"/> <expand macro="digestion"/> - <expand macro="variable_modification"/> + <expand macro="variable_modification" mod_3="true"/> <expand macro="static_modification"/> <expand macro="glyco_labile"/> <expand macro="mass_offsets"/> @@ -86,11 +86,23 @@ <xml name="msfragger_TMT"> <expand macro="search_tolerances"/> <expand macro="digestion" digest_mass_range_min="200.0"/> - <expand macro="variable_modification"/> + <expand macro="variable_modification" mod_3="true" mod_group_tmt="true"/> + <expand macro="static_modification" lysine_value="229.16293"/> + <expand macro="glyco_labile"/> + <expand macro="mass_offsets"/> + <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/> + <expand macro="open_search_options"/> + <expand macro="modeling_output"/> + <expand macro="advanced_options"/> + </xml> + <xml name="msfragger_dia_speclib_quant"> + <expand macro="search_tolerances"/> + <expand macro="digestion" allowed_missed_cleavage_1="1" allowed_missed_cleavage_2="1"/> + <expand macro="variable_modification" mod_1="true"/> <expand macro="static_modification"/> <expand macro="glyco_labile"/> <expand macro="mass_offsets"/> - <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/> + <expand macro="spectrum_processing" check_spectral_files="false"/> <expand macro="open_search_options"/> <expand macro="modeling_output"/> <expand macro="advanced_options"/> @@ -223,12 +235,11 @@ <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@" label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/> <param name="search_enzyme_cut" type="text" value="@CUT@" - label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts Default: KR"/> + label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts"/> <param name="search_enzyme_nocut" type="text" value="@NOCUT@" - label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore) Default: P"/> + label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore)"/> </xml> - <!-- wagnerr here in final param review --> - <xml name="digest" token_stricttrypsin="true" token_nonspecific="false"> + <xml name="digest" token_stricttrypsin="true" token_nonspecific="false" token_allowed_missed_cleavage="2"> <conditional name="digest"> <param name="search_enzyme" type="select" label="Protein Digestion Enzyme"> <option value="trypsin">trypsin</option> @@ -284,7 +295,7 @@ <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/> </when> <when value="nonspecific"> - <expand macro="cleavage" search_enzyme_name="nonspecific" cut="-" nocut=""/> + <expand macro="cleavage" search_enzyme_name="nonspecific" cut="@" nocut=""/> </when> <when value="custom"> <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/> @@ -305,17 +316,17 @@ <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/> </when> </conditional> - <param name="allowed_missed_cleavage" type="integer" value="2" min="0" max="5" optional="true" + <param name="allowed_missed_cleavage" type="integer" value="@ALLOWED_MISSED_CLEAVAGE@" min="0" max="5" optional="true" label="Allowed number of missed cleavages"/> - <param name="search_enzyme_sense" type="select" label="Protein Digestion Enzyme"> + <param name="search_enzyme_sense" type="select" label="Search Enzyme Sense"> <option value="C">C</option> <option value="N">N</option> </param> </xml> - <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0"> + <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0" token_allowed_missed_cleavage_1="2" token_allowed_missed_cleavage_2="2"> <section name="digestion" expanded="false" title="In-silico Digestion Parameters"> - <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@"/> + <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_1@"/> <conditional name="enzyme2"> <param name="digest2" type="select" label="Second Enzyme Digest"> <option value="no">No</option> @@ -323,7 +334,7 @@ </param> <when value="no"/> <when value="yes"> - <expand macro="digest" stricttrypsin="false" nonspecific="false"/> + <expand macro="digest" stricttrypsin="false" nonspecific="false" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_2@"/> </when> </conditional> <param name="num_enzyme_termini" type="select" label="Number of enzyme termini"> @@ -346,7 +357,11 @@ ##enzyme_1 #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name - #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut + #if $prefix.digestion.search_enzyme_cut == '__at__' + #set $msfragger_dict['search_enzyme_cut_1'] = '@' + #else + #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut + #end if #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut #if $prefix.digestion.allowed_missed_cleavage != '' #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage @@ -358,7 +373,11 @@ #if $prefix.digestion.enzyme2.digest2 == 'yes' #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name - #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut + #if $prefix.digestion.enzyme2.digest.search_enzyme_cut == '__at__' + #set $msfragger_dict['search_enzyme_cut_2'] = '@' + #else + #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut + #end if #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut #if $prefix.digestion.enzyme2.allowed_missed_cleavage != '' #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage @@ -386,27 +405,26 @@ #end if ]]></token> - <xml name="variable_modifications"> - <option value="15.99491461956 M 3">Oxidation of M (15.99491461956) modaa</option> - <option value="42.0105646837 [^ 1">Acetylation of peptide N-term (42.0105646837) modn_peptide</option> - <option value="79.96633052074999 STY 3">Phosphorylation of STY (79.96633052074999) modaa</option> - <option value="229.16293213472 n^ 1">TMT 10-plex of peptide N-term (229.16293213472) modn_peptide</option> - <option value="229.169252 n^ 1">TMT 11-plex of peptide N-term (229.169252) modn_peptide</option> - <option value="229.16293213472 S 1">TMT 10-plex of S (229.16293213472) modaa</option> - <option value="229.169252 S 1">TMT 11-plex of S (229.169252) modaa</option> - <option value="-18.0105646837 nE 1">Pyrolidone from E (-18.0105646837) modnaa_peptide</option> - </xml> - <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token> <token name="@RE_AA@">([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\])</token> <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token> <token name="@RE_MODS@">@RE_MOD@(;\s*@RE_MOD@)*</token> - <xml name="variable_modification" token_max_variable_mods_per_peptide="3"> + <xml name="variable_modification" token_max_variable_mods_per_peptide="3" token_mod_1="false" token_mod_2="false" token_mod_3="false" token_mod_4="true" token_mod_group_hla="false" token_mod_group_tmt="false"> <section name="variable_modification" expanded="false" title="Variable Modifications"> <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true" label="Maximum total number of variable modifications per peptide"/> <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications"> - <expand macro="variable_modifications"/> + <option value="15.99491461956 M 1" selected="@MOD_1@">15.99491461956 M 1</option> + <option value="15.99491461956 M 2" selected="@MOD_2@">15.99491461956 M 2</option> + <option value="15.99491461956 M 3" selected="@MOD_3@">15.99491461956 M 3</option> + <option value="42.0105646837 ntermsite^ 1" selected="@MOD_4@">42.0105646837 [^ 1</option> + <option value="-17.0265 nQ 1" selected="@MOD_GROUP_HLA@">-17.0265 nQ 1</option> + <option value="-18.0106 nE 1" selected="@MOD_GROUP_HLA@">-18.0106 nE 1</option> + <option value="119.0041 C 1" selected="@MOD_GROUP_HLA@">119.0041 C 1</option> + <option value="79.96633052074999 STY 3">79.96633052074999 STY 3</option> + <option value="229.16293213472 n^ 1" selected="@MOD_GROUP_TMT@">229.16293213472 n^ 1</option> + <option value="229.16293213472 S 1" selected="@MOD_GROUP_TMT@">229.16293213472 S 1</option> + <option value="-18.0105646837 nE 1">-18.0105646837 nE 1</option> </param> <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true" label="Enter Variable Modifications"> @@ -436,10 +454,6 @@ <option value="true">Yes</option> <option value="false">No</option> </param> - <param name="allow_multiple_variable_mods_on_residue" type="select" optional="true" label="Allow each amino acid to be modified by multiple variable modifications"> - <option value="true">Yes</option> - <option value="false">No</option> - </param> <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true" label="Maximum allowed number of modified variably modified peptides from each peptide sequence" @@ -464,184 +478,241 @@ #if $prefix.variable_modification.clip_nTerm_M != 'None' #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M #end if - #if $prefix.variable_modification.allow_multiple_variable_mods_on_residue != 'None' - #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue - #end if #if $prefix.variable_modification.max_variable_mods_combinations != "None" #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations #end if #set $vmods = [] #if $prefix.variable_modification.variable_mods_select != 'None' - #set $vmods = [x.replace(' ',',') for x in str($prefix.variable_modification.variable_mods_select).split(',')] + #set $vmods = [x.replace(' ',',').replace('ntermsite','[') for x in str($prefix.variable_modification.variable_mods_select).split(',')] #end if #if $prefix.variable_modification.variable_mods != '' #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')] #end if ]]></token> - <xml name="static_modification"> + <xml name="static_modification" token_check_cysteine="true" token_lysine_value="0.0"> <section name="static_modification" expanded="false" title="Static Modifications"> - <param name="add_Cterm_peptide" type="float" value="" optional="true" - label="Statically add mass in Da to C-terminal of peptide Default: 0.0" /> - <param name="add_Nterm_peptide" type="float" value="" optional="true" - label="Statically add mass in Da to N-terminal of peptide Default: 0.0" /> - <param name="add_Cterm_protein" type="float" value="" optional="true" - label="Statically add mass in Da to C-terminal of protein Default: 0.0" /> - <param name="add_Nterm_protein" type="float" value="" optional="true" - label="Statically add mass in Da to N-terminal of protein Default: 0.0" /> - <param name="add_A_alanine" type="float" value="" optional="true" - label="Statically add mass in Da to A (alanine) Default: 0.0" /> - <param name="add_R_arginine" type="float" value="" optional="true" - label="Statically add mass in Da to R (arginine) Default: 0.0" /> - <param name="add_N_asparagine" type="float" value="" optional="true" - label="Statically add mass in Da to N (asparagine) Default: 0.0" /> - <param name="add_D_aspartic_acid" type="float" value="" optional="true" - label="Statically add mass in Da to D (aspartic_acid) Default: 0.0" /> - <param name="add_C_cysteine" type="float" value="" optional="true" - label="Statically add mass in Da to C (cysteine) Default: 0.0" /> - <param name="add_E_glutamic_acid" type="float" value="" optional="true" - label="Statically add mass in Da to E (glutamic_acid) Default: 0.0" /> - <param name="add_Q_glutamine" type="float" value="" optional="true" - label="Statically add mass in Da to Q (glutamine) Default: 0.0" /> - <param name="add_G_glycine" type="float" value="" optional="true" - label="Statically add mass in Da to G (glycine) Default: 0.0" /> - <param name="add_H_histidine" type="float" value="" optional="true" - label="Statically add mass in Da to H (histidine) Default: 0.0" /> - <param name="add_I_isoleucine" type="float" value="" optional="true" - label="Statically add mass in Da to I (isoleucine) Default: 0.0" /> - <param name="add_L_leucine" type="float" value="" optional="true" - label="Statically add mass in Da to L (leucine) Default: 0.0" /> - <param name="add_K_lysine" type="float" value="" optional="true" - label="Statically add mass in Da to K (lysine) Default: 0.0" /> - <param name="add_M_methionine" type="float" value="" optional="true" - label="Statically add mass in Da to M (methionine) Default: 0.0" /> - <param name="add_F_phenylalanine" type="float" value="" optional="true" - label="Statically add mass in Da to F (phenylalanine) Default: 0.0" /> - <param name="add_P_proline" type="float" value="" optional="true" - label="Statically add mass in Da to P (proline) Default: 0.0" /> - <param name="add_S_serine" type="float" value="" optional="true" - label="Statically add mass in Da to S (serine) Default: 0.0" /> - <param name="add_T_threonine" type="float" value="" optional="true" - label="Statically add mass in Da to T (threonine) Default: 0.0" /> - <param name="add_W_tryptophan" type="float" value="" optional="true" - label="Statically add mass in Da to W (tryptophan) Default: 0.0" /> - <param name="add_Y_tyrosine" type="float" value="" optional="true" - label="Statically add mass in Da to Y (tyrosine) Default: 0.0" /> - <param name="add_V_valine" type="float" value="" optional="true" - label="Statically add mass in Da to V (valine) Default: 0.0" /> - <param name="add_B_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to B (iuser_amino_acid) Default: 0.0" /> - <param name="add_J_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to J (iuser_amino_acid) Default: 0.0" /> - <param name="add_O_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to O (user_amino_acid) Default: 0.0" /> - <param name="add_U_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to U (iuser_amino_acid) Default: 0.0" /> - <param name="add_X_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to X (iuser_amino_acid) Default: 0.0" /> - <param name="add_Z_user_amino_acid" type="float" value="" optional="true" - label="Statically add mass in Da to Z (iuser_amino_acid) Default: 0.0" /> + <param name="add_Cterm_peptide_bool" type="boolean" checked="true" + label="Statically add mass in Da to C-terminal of peptide"/> + <param name="add_Cterm_peptide" type="float" value="0.0" + label="Statically add mass in Da to C-terminal of peptide" /> + + <param name="add_Nterm_peptide_bool" type="boolean" checked="true" + label="Statically add mass in Da to N-terminal of peptide"/> + <param name="add_Nterm_peptide" type="float" value="0.0" + label="Statically add mass in Da to N-terminal of peptide" /> + + <param name="add_Cterm_protein_bool" type="boolean" checked="true" + label="Statically add mass in Da to C-terminal of protein"/> + <param name="add_Cterm_protein" type="float" value="0.0" + label="Statically add mass in Da to C-terminal of protein" /> + + <param name="add_Nterm_protein_bool" type="boolean" checked="true" + label="Statically add mass in Da to N-terminal of protein"/> + <param name="add_Nterm_protein" type="float" value="0.0" + label="Statically add mass in Da to N-terminal of protein" /> + + <param name="add_A_alanine_bool" type="boolean" checked="true" + label="Statically add mass in Da to A (alanine)"/> + <param name="add_A_alanine" type="float" value="0.0" + label="Statically add mass in Da to A (alanine)" /> + + <param name="add_R_arginine_bool" type="boolean" checked="true" + label="Statically add mass in Da to R (arginine)"/> + <param name="add_R_arginine" type="float" value="0.0" + label="Statically add mass in Da to R (arginine)" /> + + <param name="add_N_asparagine_bool" type="boolean" checked="true" + label="Statically add mass in Da to N (asparagine)"/> + <param name="add_N_asparagine" type="float" value="0.0" + label="Statically add mass in Da to N (asparagine)" /> + + <param name="add_D_aspartic_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to D (aspartic_acid)"/> + <param name="add_D_aspartic_acid" type="float" value="0.0" + label="Statically add mass in Da to D (aspartic_acid)" /> + + <param name="add_C_cysteine_bool" type="boolean" checked="@CHECK_CYSTEINE@" + label="Statically add mass in Da to C (cysteine)"/> + <param name="add_C_cysteine" type="float" value="57.02146" + label="Statically add mass in Da to C (cysteine)" /> + + <param name="add_E_glutamic_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to E (glutamic_acid)"/> + <param name="add_E_glutamic_acid" type="float" value="0.0" + label="Statically add mass in Da to E (glutamic_acid)" /> + + <param name="add_Q_glutamine_bool" type="boolean" checked="true" + label="Statically add mass in Da to Q (glutamine)"/> + <param name="add_Q_glutamine" type="float" value="0.0" + label="Statically add mass in Da to Q (glutamine)" /> + + <param name="add_G_glycine_bool" type="boolean" checked="true" + label="Statically add mass in Da to G (glycine)"/> + <param name="add_G_glycine" type="float" value="0.0" + label="Statically add mass in Da to G (glycine)" /> + + <param name="add_H_histidine_bool" type="boolean" checked="true" + label="Statically add mass in Da to H (histidine)"/> + <param name="add_H_histidine" type="float" value="0.0" + label="Statically add mass in Da to H (histidine)" /> + + <param name="add_I_isoleucine_bool" type="boolean" checked="true" + label="Statically add mass in Da to I (isoleucine)"/> + <param name="add_I_isoleucine" type="float" value="0.0" + label="Statically add mass in Da to I (isoleucine)" /> + + <param name="add_L_leucine_bool" type="boolean" checked="true" + label="Statically add mass in Da to L (leucine)"/> + <param name="add_L_leucine" type="float" value="0.0" + label="Statically add mass in Da to L (leucine)" /> + + <param name="add_K_lysine_bool" type="boolean" checked="true" + label="Statically add mass in Da to K (lysine)"/> + <param name="add_K_lysine" type="float" value="@LYSINE_VALUE@" + label="Statically add mass in Da to K (lysine)" /> + + <param name="add_M_methionine_bool" type="boolean" checked="true" + label="Statically add mass in Da to M (methionine)"/> + <param name="add_M_methionine" type="float" value="0.0" + label="Statically add mass in Da to M (methionine)" /> + + <param name="add_F_phenylalanine_bool" type="boolean" checked="true" + label="Statically add mass in Da to F (phenylalanine)"/> + <param name="add_F_phenylalanine" type="float" value="0.0" + label="Statically add mass in Da to F (phenylalanine)" /> + + <param name="add_P_proline_bool" type="boolean" checked="true" + label="Statically add mass in Da to P (proline)"/> + <param name="add_P_proline" type="float" value="0.0" + label="Statically add mass in Da to P (proline)" /> + + <param name="add_S_serine_bool" type="boolean" checked="true" + label="Statically add mass in Da to S (serine)"/> + <param name="add_S_serine" type="float" value="0.0" + label="Statically add mass in Da to S (serine)" /> + + <param name="add_T_threonine_bool" type="boolean" checked="true" + label="Statically add mass in Da to T (threonine)"/> + <param name="add_T_threonine" type="float" value="0.0" + label="Statically add mass in Da to T (threonine)" /> + + <param name="add_W_tryptophan_bool" type="boolean" checked="true" + label="Statically add mass in Da to W (tryptophan)"/> + <param name="add_W_tryptophan" type="float" value="0.0" + label="Statically add mass in Da to W (tryptophan)" /> + + <param name="add_Y_tyrosine_bool" type="boolean" checked="true" + label="Statically add mass in Da to Y (tyrosine)"/> + <param name="add_Y_tyrosine" type="float" value="0.0" + label="Statically add mass in Da to Y (tyrosine)" /> + + <param name="add_V_valine_bool" type="boolean" checked="true" + label="Statically add mass in Da to V (valine)"/> + <param name="add_V_valine" type="float" value="0.0" + label="Statically add mass in Da to V (valine)" /> + + <param name="add_B_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to B (iuser_amino_acid)"/> + <param name="add_B_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to B (iuser_amino_acid)" /> + + <param name="add_J_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to J (iuser_amino_acid)"/> + <param name="add_J_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to J (iuser_amino_acid)" /> + + <param name="add_O_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to O (user_amino_acid)"/> + <param name="add_O_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to O (user_amino_acid)" /> + + <param name="add_U_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to U (iuser_amino_acid)"/> + <param name="add_U_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to U (iuser_amino_acid)" /> + + <param name="add_X_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to X (iuser_amino_acid)"/> + <param name="add_X_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to X (iuser_amino_acid)" /> + + <param name="add_Z_user_amino_acid_bool" type="boolean" checked="true" + label="Statically add mass in Da to Z (iuser_amino_acid)"/> + <param name="add_Z_user_amino_acid" type="float" value="0.0" + label="Statically add mass in Da to Z (iuser_amino_acid)" /> </section> </xml> <token name="@STATIC_MODIFICATION@"><![CDATA[ - #set $fmods = {} - #if $prefix.static_modification.add_Cterm_peptide != '' - #set $fmods['Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide - #end if - #if $prefix.static_modification.add_Nterm_peptide != '' - #set $fmods['Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide - #end if - #if $prefix.static_modification.add_Cterm_protein != '' - #set $fmods['Cterm_protein'] = $prefix.static_modification.add_Cterm_protein - #end if - #if $prefix.static_modification.add_Nterm_protein != '' - #set $fmods['Nterm_protein'] = $prefix.static_modification.add_Nterm_protein - #end if - #if $prefix.static_modification.add_G_glycine != '' - #set $fmods['G_glycine'] = $prefix.static_modification.add_G_glycine - #end if - #if $prefix.static_modification.add_A_alanine != '' - #set $fmods['A_alanine'] = $prefix.static_modification.add_A_alanine - #end if - #if $prefix.static_modification.add_S_serine != '' - #set $fmods['S_serine'] = $prefix.static_modification.add_S_serine - #end if - #if $prefix.static_modification.add_P_proline != '' - #set $fmods['P_proline'] = $prefix.static_modification.add_P_proline - #end if - #if $prefix.static_modification.add_V_valine != '' - #set $fmods['V_valine'] = $prefix.static_modification.add_V_valine - #end if - #if $prefix.static_modification.add_T_threonine != '' - #set $fmods['T_threonine'] = $prefix.static_modification.add_T_threonine - #end if - #if $prefix.static_modification.add_C_cysteine != '' - #set $fmods['C_cysteine'] = $prefix.static_modification.add_C_cysteine - #end if - #if $prefix.static_modification.add_L_leucine != '' - #set $fmods['L_leucine'] = $prefix.static_modification.add_L_leucine - #end if - #if $prefix.static_modification.add_I_isoleucine != '' - #set $fmods['I_isoleucine'] = $prefix.static_modification.add_I_isoleucine - #end if - #if $prefix.static_modification.add_N_asparagine != '' - #set $fmods['N_asparagine'] = $prefix.static_modification.add_N_asparagine - #end if - #if $prefix.static_modification.add_D_aspartic_acid != '' - #set $fmods['D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid - #end if - #if $prefix.static_modification.add_Q_glutamine != '' - #set $fmods['Q_glutamine'] = $prefix.static_modification.add_Q_glutamine - #end if - #if $prefix.static_modification.add_K_lysine != '' - #set $fmods['K_lysine'] = $prefix.static_modification.add_K_lysine - #end if - #if $prefix.static_modification.add_E_glutamic_acid != '' - #set $fmods['E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid - #end if - #if $prefix.static_modification.add_M_methionine != '' - #set $fmods['M_methionine'] = $prefix.static_modification.add_M_methionine - #end if - #if $prefix.static_modification.add_H_histidine != '' - #set $fmods['H_histidine'] = $prefix.static_modification.add_H_histidine - #end if - #if $prefix.static_modification.add_F_phenylalanine != '' - #set $fmods['F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine - #end if - #if $prefix.static_modification.add_R_arginine != '' - #set $fmods['R_arginine'] = $prefix.static_modification.add_R_arginine - #end if - #if $prefix.static_modification.add_Y_tyrosine != '' - #set $fmods['Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine - #end if - #if $prefix.static_modification.add_W_tryptophan != '' - #set $fmods['W_tryptophan'] = $prefix.static_modification.add_W_tryptophan - #end if - #* - #if $prefix.static_modification.add_B_user_amino_acid != '' - #set $fmods['B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid - #end if - #if $prefix.static_modification.add_J_user_amino_acid != '' - #set $fmods['J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid - #end if - #if $prefix.static_modification.add_O_user_amino_acid != '' - #set $fmods['O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid - #end if - #if $prefix.static_modification.add_U_user_amino_acid != '' - #set $fmods['U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid - #end if - #if $prefix.static_modification.add_X_user_amino_acid != '' - #set $fmods['X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid - #end if - #if $prefix.static_modification.add_Z_user_amino_acid != '' - #set $fmods['Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid - #end if - *# + #set $fmod_vals = {} + #set $fmod_vals['add_Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide + #set $fmod_vals['add_Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide + #set $fmod_vals['add_Cterm_protein'] = $prefix.static_modification.add_Cterm_protein + #set $fmod_vals['add_Nterm_protein'] = $prefix.static_modification.add_Nterm_protein + #set $fmod_vals['add_G_glycine'] = $prefix.static_modification.add_G_glycine + #set $fmod_vals['add_A_alanine'] = $prefix.static_modification.add_A_alanine + #set $fmod_vals['add_S_serine'] = $prefix.static_modification.add_S_serine + #set $fmod_vals['add_P_proline'] = $prefix.static_modification.add_P_proline + #set $fmod_vals['add_V_valine'] = $prefix.static_modification.add_V_valine + #set $fmod_vals['add_T_threonine'] = $prefix.static_modification.add_T_threonine + #set $fmod_vals['add_C_cysteine'] = $prefix.static_modification.add_C_cysteine + #set $fmod_vals['add_L_leucine'] = $prefix.static_modification.add_L_leucine + #set $fmod_vals['add_I_isoleucine'] = $prefix.static_modification.add_I_isoleucine + #set $fmod_vals['add_N_asparagine'] = $prefix.static_modification.add_N_asparagine + #set $fmod_vals['add_D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid + #set $fmod_vals['add_Q_glutamine'] = $prefix.static_modification.add_Q_glutamine + #set $fmod_vals['add_K_lysine'] = $prefix.static_modification.add_K_lysine + #set $fmod_vals['add_E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid + #set $fmod_vals['add_M_methionine'] = $prefix.static_modification.add_M_methionine + #set $fmod_vals['add_H_histidine'] = $prefix.static_modification.add_H_histidine + #set $fmod_vals['add_F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine + #set $fmod_vals['add_R_arginine'] = $prefix.static_modification.add_R_arginine + #set $fmod_vals['add_Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine + #set $fmod_vals['add_W_tryptophan'] = $prefix.static_modification.add_W_tryptophan + #set $fmod_vals['add_B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid + #set $fmod_vals['add_J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid + #set $fmod_vals['add_O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid + #set $fmod_vals['add_U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid + #set $fmod_vals['add_X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid + #set $fmod_vals['add_Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid + + #set $fmod_bools = {} + #set $fmod_bools['add_Cterm_peptide_bool'] = $prefix.static_modification.add_Cterm_peptide_bool + #set $fmod_bools['add_Nterm_peptide_bool'] = $prefix.static_modification.add_Nterm_peptide_bool + #set $fmod_bools['add_Cterm_protein_bool'] = $prefix.static_modification.add_Cterm_protein_bool + #set $fmod_bools['add_Nterm_protein_bool'] = $prefix.static_modification.add_Nterm_protein_bool + #set $fmod_bools['add_G_glycine_bool'] = $prefix.static_modification.add_G_glycine_bool + #set $fmod_bools['add_A_alanine_bool'] = $prefix.static_modification.add_A_alanine_bool + #set $fmod_bools['add_S_serine_bool'] = $prefix.static_modification.add_S_serine_bool + #set $fmod_bools['add_P_proline_bool'] = $prefix.static_modification.add_P_proline_bool + #set $fmod_bools['add_V_valine_bool'] = $prefix.static_modification.add_V_valine_bool + #set $fmod_bools['add_T_threonine_bool'] = $prefix.static_modification.add_T_threonine_bool + #set $fmod_bools['add_C_cysteine_bool'] = $prefix.static_modification.add_C_cysteine_bool + #set $fmod_bools['add_L_leucine_bool'] = $prefix.static_modification.add_L_leucine_bool + #set $fmod_bools['add_I_isoleucine_bool'] = $prefix.static_modification.add_I_isoleucine_bool + #set $fmod_bools['add_N_asparagine_bool'] = $prefix.static_modification.add_N_asparagine_bool + #set $fmod_bools['add_D_aspartic_acid_bool'] = $prefix.static_modification.add_D_aspartic_acid_bool + #set $fmod_bools['add_Q_glutamine_bool'] = $prefix.static_modification.add_Q_glutamine_bool + #set $fmod_bools['add_K_lysine_bool'] = $prefix.static_modification.add_K_lysine_bool + #set $fmod_bools['add_E_glutamic_acid_bool'] = $prefix.static_modification.add_E_glutamic_acid_bool + #set $fmod_bools['add_M_methionine_bool'] = $prefix.static_modification.add_M_methionine_bool + #set $fmod_bools['add_H_histidine_bool'] = $prefix.static_modification.add_H_histidine_bool + #set $fmod_bools['add_F_phenylalanine_bool'] = $prefix.static_modification.add_F_phenylalanine_bool + #set $fmod_bools['add_R_arginine_bool'] = $prefix.static_modification.add_R_arginine_bool + #set $fmod_bools['add_Y_tyrosine_bool'] = $prefix.static_modification.add_Y_tyrosine_bool + #set $fmod_bools['add_W_tryptophan_bool'] = $prefix.static_modification.add_W_tryptophan_bool + #set $fmod_bools['add_B_user_amino_acid_bool'] = $prefix.static_modification.add_B_user_amino_acid_bool + #set $fmod_bools['add_J_user_amino_acid_bool'] = $prefix.static_modification.add_J_user_amino_acid_bool + #set $fmod_bools['add_O_user_amino_acid_bool'] = $prefix.static_modification.add_O_user_amino_acid_bool + #set $fmod_bools['add_U_user_amino_acid_bool'] = $prefix.static_modification.add_U_user_amino_acid_bool + #set $fmod_bools['add_X_user_amino_acid_bool'] = $prefix.static_modification.add_X_user_amino_acid_bool + #set $fmod_bools['add_Z_user_amino_acid_bool'] = $prefix.static_modification.add_Z_user_amino_acid_bool + ]]></token> - <xml name="spectrum_processing" token_mode_selected="false" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false"> + <xml name="spectrum_processing" token_mode_selected="true" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false" token_check_spectral_files="true"> <section name="spectrum_processing" expanded="false" title="Spectrum Processing"> - <param name="precursor_mass_mode" type="select" optional="true" label="Precursor mass mode"> + <param name="precursor_mass_mode" type="select" label="Precursor mass mode"> <option value="isolated" selected="@MODE_ISOLATED@">isolated</option> <option value="selected" selected="@MODE_SELECTED@">selected</option> <option value="corrected" selected="@MODE_CORRECTED@">corrected</option> @@ -683,7 +754,7 @@ <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option> <option value="1" selected="@TRANSFORM_SQRT@">Square root</option> </param> - <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Check spectral files"/> + <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="@CHECK_SPECTRAL_FILES@" label="Check spectral files"/> <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/> <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/> <param name="activation_types" type="select" optional="true" label="Activation Type Filter"> @@ -770,14 +841,6 @@ <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true" label="Multiplies expect value of PSMs in the zero-bin during results ordering" help="(set to less than 1 for boosting) Default: 1.0" /> - <param name="add_topN_complementary" type="integer" value="" min="0" optional="true" - label="Insert complementary ions corresponding to the top N most intense fragments in each experimental spectra." > - <help> - Useful for recovery of modified peptides near C-terminal in open search. - Should be set to 0 (disabled) otherwise. - Default: 0 - </help> - </param> <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" /> <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" /> <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@" @@ -798,9 +861,6 @@ #if $prefix.open_search.zero_bin_mult_expect != '' #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect #end if - #if $prefix.open_search.add_topN_complementary != '' - #set $msfragger_dict['add_topN_complementary'] = $prefix.open_search.add_topN_complementary - #end if #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')' ]]></token> @@ -938,7 +998,7 @@ <!-- Formatting options for output files. --> <xml name="advanced_options"> <section name="advanced_options" expanded="false" title="Advanced Options"> - <param name="output_format" type="select" multiple="true" label="output format"> + <param name="output_format" type="select" label="output format"> <option value="pepXML">PEPXML</option> <option value="tsv">TSV</option> <option value="tsv_pepXML">TSV_PEPXML</option> @@ -955,7 +1015,6 @@ label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" /> <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/> - <param name="write_uncalibrated_mgf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write uncalibrated MGF"/> <param name="group_variable" type="select" optional="true" label="Group variable"> <option value="0">None</option> <option value="1">Number of enzymatic termini</option> @@ -966,16 +1025,14 @@ <!-- Does not enter into msfragger_dict, instead produces configuration text. --> <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[ - #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format.__str__.replace(',mgf','').replace(',','_') - #if $prefix.advanced_options.output_report_topN != '' - #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN - #end if + #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format + #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins + #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect #if $prefix.advanced_options.output_max_expect != '' #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect #end if #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml - #set $msfragger_dict['write_uncalibrated_mgf'] = $prefix.advanced_options.write_uncalibrated_mgf #if $prefix.advanced_options.group_variable != 'None' #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable #end if