Mercurial > repos > galaxyp > openms_speclibsearcher
diff SpecLibSearcher.xml @ 9:2d6e49acbb56 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:35:13 +0000 |
| parents | 3aa3b656e624 |
| children |
line wrap: on
line diff
--- a/SpecLibSearcher.xml Thu Dec 01 19:12:08 2022 +0000 +++ b/SpecLibSearcher.xml Fri Jun 14 21:35:13 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Identification]--> +<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]--> <tool id="SpecLibSearcher" name="SpecLibSearcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.</description> + <description>Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library</description> <macros> <token name="@EXECUTABLE@">SpecLibSearcher</token> <import>macros.xml</import> @@ -17,12 +16,12 @@ mkdir in_cond.in && #if $in_cond.in_select == "no" mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && -${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} +${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])} #else -ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && +cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && #end if mkdir lib && -ln -s '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && +cp '$lib' 'lib/${re.sub("[^\w\-_]", "_", $lib.element_identifier)}.$gxy2omsext($lib.ext)' && mkdir out && mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && @@ -59,14 +58,14 @@ <option value="yes">Yes: process each dataset in an independent job</option> </param> <when value="no"> - <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" multiple="true" label="Input files" help=" select mzml data sets(s)"/> </when> <when value="yes"> - <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input files" help=" select mzml data sets(s)"/> + <param argument="-in" type="data" format="mzml" label="Input files" help=" select mzml data sets(s)"/> </when> </conditional> - <param argument="-lib" type="data" format="msp" optional="false" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> - <param argument="-compare_function" type="select" optional="true" label="function for similarity comparison" help=""> + <param argument="-lib" type="data" format="msp" label="searchable spectral library (MSP format)" help=" select msp data sets(s)"/> + <param argument="-compare_function" type="select" label="function for similarity comparison" help=""> <option value="PeakAlignment">PeakAlignment</option> <option value="SpectrumAlignmentScore">SpectrumAlignmentScore</option> <option value="SpectrumCheapDPCorr">SpectrumCheapDPCorr</option> @@ -76,32 +75,32 @@ <expand macro="list_string_san" name="compare_function"/> </param> <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> - <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Width of precursor mass tolerance window" help=""/> - <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> + <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Width of precursor mass tolerance window" help=""/> + <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> - <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="2" label="Minimum precursor charge to be considered" help=""/> - <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="5" label="Maximum precursor charge to be considered" help=""/> - <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="min_charge" argument="-precursor:min_charge" type="integer" value="2" label="Minimum precursor charge to be considered" help=""/> + <param name="max_charge" argument="-precursor:max_charge" type="integer" value="5" label="Maximum precursor charge to be considered" help=""/> + <param name="isotopes" argument="-precursor:isotopes" type="text" value="0 1" label="Corrects for mono-isotopic peak misassignments" help="(E.g.: 1 = prec. may be misassigned to first isotopic peak) (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_integer_valsan" name="isotopes"/> </param> </section> <section name="fragment" title="Fragments (Product Ion) Options" help="" expanded="false"> - <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance" help=""/> + <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance" help=""/> </section> <section name="report" title="Reporting Options" help="" expanded="false"> - <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="10" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> + <param name="top_hits" argument="-report:top_hits" type="integer" value="10" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> </section> <section name="filter" title="Filtering options" help="Most are especially useful when the query spectra are raw" expanded="false"> - <param name="remove_peaks_below_threshold" argument="-filter:remove_peaks_below_threshold" type="float" optional="true" value="2.01" label="All peaks of a query spectrum with intensities below <threshold> will be zeroed" help=""/> - <param name="min_peaks" argument="-filter:min_peaks" type="integer" optional="true" value="5" label="required minimum number of peaks for a query spectrum" help=""/> - <param name="max_peaks" argument="-filter:max_peaks" type="integer" optional="true" value="150" label="Use only the top <number> of peaks" help=""/> - <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" optional="true" value="1000" label="Remove all peaks which are lower than 1/<number> of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/> + <param name="remove_peaks_below_threshold" argument="-filter:remove_peaks_below_threshold" type="float" value="2.01" label="All peaks of a query spectrum with intensities below <threshold> will be zeroed" help=""/> + <param name="min_peaks" argument="-filter:min_peaks" type="integer" value="5" label="required minimum number of peaks for a query spectrum" help=""/> + <param name="max_peaks" argument="-filter:max_peaks" type="integer" value="150" label="Use only the top <number> of peaks" help=""/> + <param name="cut_peaks_below" argument="-filter:cut_peaks_below" type="integer" value="1000" label="Remove all peaks which are lower than 1/<number> of the highest peaks" help="Default equals all peaks which are lower than 0.001 of the maximum intensity peak"/> </section> <section name="modifications" title="Modifications Options" help="" expanded="false"> - <param name="fixed" argument="-modifications:fixed" multiple="true" type="select" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> + <param name="fixed" argument="-modifications:fixed" type="select" multiple="true" optional="true" label="Fixed modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -111,6 +110,10 @@ <option value="2-succinyl (C)">2-succinyl (C)</option> <option value="2HPG (R)">2HPG (R)</option> <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> + <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option> + <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option> + <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option> + <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option> <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> <option value="3sulfo (N-term)">3sulfo (N-term)</option> <option value="4-ONE (C)">4-ONE (C)</option> @@ -200,6 +203,7 @@ <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> + <option value="Andro-H2O (C)">Andro-H2O (C)</option> <option value="Archaeol (C)">Archaeol (C)</option> <option value="Arg (N-term)">Arg (N-term)</option> <option value="Arg->Ala (R)">Arg->Ala (R)</option> @@ -303,6 +307,7 @@ <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> + <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option> <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> @@ -335,7 +340,6 @@ <option value="BITC (N-term)">BITC (N-term)</option> <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> - <option value="Bodipy (C)">Bodipy (C)</option> <option value="Brij35 (N-term)">Brij35 (N-term)</option> <option value="Brij58 (N-term)">Brij58 (N-term)</option> <option value="Bromo (F)">Bromo (F)</option> @@ -767,9 +771,9 @@ <option value="Dehydrated (T)">Dehydrated (T)</option> <option value="Dehydrated (Y)">Dehydrated (Y)</option> <option value="Dehydro (C)">Dehydro (C)</option> + <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option> <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> - <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option> <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> @@ -779,7 +783,6 @@ <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> - <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option> <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> @@ -791,6 +794,7 @@ <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> + <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option> <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> @@ -1363,7 +1367,6 @@ <option value="Ethanolyl (C)">Ethanolyl (C)</option> <option value="Ethanolyl (K)">Ethanolyl (K)</option> <option value="Ethanolyl (R)">Ethanolyl (R)</option> - <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option> <option value="Ethyl (C-term)">Ethyl (C-term)</option> <option value="Ethyl (D)">Ethyl (D)</option> <option value="Ethyl (E)">Ethyl (E)</option> @@ -1457,6 +1460,7 @@ <option value="Gln->Xle (Q)">Gln->Xle (Q)</option> <option value="Glu (E)">Glu (E)</option> <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> + <option value="Glu+O(2) (H)">Glu+O(2) (H)</option> <option value="Glu->Ala (E)">Glu->Ala (E)</option> <option value="Glu->Arg (E)">Glu->Arg (E)</option> <option value="Glu->Asn (E)">Glu->Asn (E)</option> @@ -1471,7 +1475,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> <option value="Glu->Thr (E)">Glu->Thr (E)</option> @@ -1495,6 +1498,7 @@ <option value="Gly (K)">Gly (K)</option> <option value="Gly (S)">Gly (S)</option> <option value="Gly (T)">Gly (T)</option> + <option value="Gly+O(2) (H)">Gly+O(2) (H)</option> <option value="Gly->Ala (G)">Gly->Ala (G)</option> <option value="Gly->Arg (G)">Gly->Arg (G)</option> <option value="Gly->Asn (G)">Gly->Asn (G)</option> @@ -1885,6 +1889,7 @@ <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> + <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option> <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> @@ -1896,6 +1901,9 @@ <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> + <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option> + <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option> + <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option> <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> @@ -1951,6 +1959,7 @@ <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> + <option value="His+O(2) (H)">His+O(2) (H)</option> <option value="His->Ala (H)">His->Ala (H)</option> <option value="His->Arg (H)">His->Arg (H)</option> <option value="His->Asn (H)">His->Asn (H)</option> @@ -2088,11 +2097,14 @@ <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> + <option value="Kdo (S)">Kdo (S)</option> + <option value="Kdo (T)">Kdo (T)</option> <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> + <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option> <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> @@ -2177,13 +2189,16 @@ <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> + <option value="LG-pyrrole (C)">LG-pyrrole (C)</option> <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> <option value="Lipoyl (K)">Lipoyl (K)</option> <option value="LRGG (K)">LRGG (K)</option> <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> + <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option> <option value="Lys (N-term)">Lys (N-term)</option> + <option value="Lys+O(2) (H)">Lys+O(2) (H)</option> <option value="Lys->Ala (K)">Lys->Ala (K)</option> <option value="Lys->Allysine (K)">Lys->Allysine (K)</option> <option value="Lys->AminoadipicAcid (K)">Lys->AminoadipicAcid (K)</option> @@ -2218,6 +2233,7 @@ <option value="Malonyl (C)">Malonyl (C)</option> <option value="Malonyl (K)">Malonyl (K)</option> <option value="Malonyl (S)">Malonyl (S)</option> + <option value="MBS+peptide (C)">MBS+peptide (C)</option> <option value="MDCC (C)">MDCC (C)</option> <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> <option value="Menadione (C)">Menadione (C)</option> @@ -2229,6 +2245,7 @@ <option value="MesitylOxide (H)">MesitylOxide (H)</option> <option value="MesitylOxide (K)">MesitylOxide (K)</option> <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> + <option value="Met+O(2) (H)">Met+O(2) (H)</option> <option value="Met->Aha (M)">Met->Aha (M)</option> <option value="Met->Ala (M)">Met->Ala (M)</option> <option value="Met->Arg (M)">Met->Arg (M)</option> @@ -2412,7 +2429,6 @@ <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> - <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option> <option value="NP40 (N-term)">NP40 (N-term)</option> <option value="NQIGG (K)">NQIGG (K)</option> <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> @@ -2500,6 +2516,10 @@ <option value="Phe->Tyr (F)">Phe->Tyr (F)</option> <option value="Phe->Val (F)">Phe->Val (F)</option> <option value="Phe->Xle (F)">Phe->Xle (F)</option> + <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option> + <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option> + <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option> + <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option> <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> @@ -2514,6 +2534,7 @@ <option value="Phospho (Y)">Phospho (Y)</option> <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> + <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option> <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> @@ -2545,6 +2566,7 @@ <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> <option value="Piperidine (K)">Piperidine (K)</option> <option value="Piperidine (N-term)">Piperidine (N-term)</option> + <option value="Pro+O(2) (H)">Pro+O(2) (H)</option> <option value="Pro->Ala (P)">Pro->Ala (P)</option> <option value="Pro->Arg (P)">Pro->Arg (P)</option> <option value="Pro->Asn (P)">Pro->Asn (P)</option> @@ -2622,18 +2644,30 @@ <option value="QTGG (K)">QTGG (K)</option> <option value="Quinone (W)">Quinone (W)</option> <option value="Quinone (Y)">Quinone (Y)</option> + <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option> + <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option> + <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option> + <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option> + <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option> + <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option> + <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option> + <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option> + <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option> + <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option> + <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option> + <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option> + <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option> + <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option> + <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option> + <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option> + <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option> + <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option> + <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option> + <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option> <option value="Retinylidene (K)">Retinylidene (K)</option> <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> - <option value="RNPXlink2 (F)">RNPXlink2 (F)</option> - <option value="RNPXlink2 (K)">RNPXlink2 (K)</option> - <option value="RNPXlink2 (L)">RNPXlink2 (L)</option> - <option value="RNPXlink3 (C)">RNPXlink3 (C)</option> - <option value="RNPXlink3 (F)">RNPXlink3 (F)</option> - <option value="RNPXlink4 (C)">RNPXlink4 (C)</option> - <option value="RNPXlink5 (F)">RNPXlink5 (F)</option> - <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option> <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> <option value="Saligenin (H)">Saligenin (H)</option> @@ -2661,6 +2695,9 @@ <option value="shTMT (K)">shTMT (K)</option> <option value="shTMT (N-term)">shTMT (N-term)</option> <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> + <option value="shTMTpro (K)">shTMTpro (K)</option> + <option value="shTMTpro (N-term)">shTMTpro (N-term)</option> + <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option> <option value="SMA (K)">SMA (K)</option> <option value="SMA (N-term)">SMA (N-term)</option> <option value="spermidine (Q)">spermidine (Q)</option> @@ -2836,7 +2873,6 @@ <option value="Tyr->Trp (Y)">Tyr->Trp (Y)</option> <option value="Tyr->Val (Y)">Tyr->Val (Y)</option> <option value="Tyr->Xle (Y)">Tyr->Xle (Y)</option> - <option value="Ub-amide (C)">Ub-amide (C)</option> <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> <option value="Ub-VME (C)">Ub-VME (C)</option> @@ -3031,7 +3067,7 @@ <option value="ZQG (K)">ZQG (K)</option> <expand macro="list_string_san" name="fixed"/> </param> - <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> + <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Oxidation (M)'"> <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option> <option value="15N-oxobutanoic (Protein N-term S)">15N-oxobutanoic (Protein N-term S)</option> <option value="15N-oxobutanoic (Protein N-term T)">15N-oxobutanoic (Protein N-term T)</option> @@ -3041,6 +3077,10 @@ <option value="2-succinyl (C)">2-succinyl (C)</option> <option value="2HPG (R)">2HPG (R)</option> <option value="3-deoxyglucosone (R)">3-deoxyglucosone (R)</option> + <option value="3-hydroxybenzyl-phosphate (K)">3-hydroxybenzyl-phosphate (K)</option> + <option value="3-hydroxybenzyl-phosphate (S)">3-hydroxybenzyl-phosphate (S)</option> + <option value="3-hydroxybenzyl-phosphate (T)">3-hydroxybenzyl-phosphate (T)</option> + <option value="3-hydroxybenzyl-phosphate (Y)">3-hydroxybenzyl-phosphate (Y)</option> <option value="3-phosphoglyceryl (K)">3-phosphoglyceryl (K)</option> <option value="3sulfo (N-term)">3sulfo (N-term)</option> <option value="4-ONE (C)">4-ONE (C)</option> @@ -3130,6 +3170,7 @@ <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> + <option value="Andro-H2O (C)">Andro-H2O (C)</option> <option value="Archaeol (C)">Archaeol (C)</option> <option value="Arg (N-term)">Arg (N-term)</option> <option value="Arg->Ala (R)">Arg->Ala (R)</option> @@ -3233,6 +3274,7 @@ <option value="Biotin-phenacyl (H)">Biotin-phenacyl (H)</option> <option value="Biotin-phenacyl (S)">Biotin-phenacyl (S)</option> <option value="Biotin-tyramide (Y)">Biotin-tyramide (Y)</option> + <option value="Biotin:Aha-DADPS (M)">Biotin:Aha-DADPS (M)</option> <option value="Biotin:Cayman-10013 (C)">Biotin:Cayman-10013 (C)</option> <option value="Biotin:Cayman-10141 (C)">Biotin:Cayman-10141 (C)</option> <option value="Biotin:Invitrogen-M1602 (C)">Biotin:Invitrogen-M1602 (C)</option> @@ -3265,7 +3307,6 @@ <option value="BITC (N-term)">BITC (N-term)</option> <option value="BMP-piperidinol (C)">BMP-piperidinol (C)</option> <option value="BMP-piperidinol (M)">BMP-piperidinol (M)</option> - <option value="Bodipy (C)">Bodipy (C)</option> <option value="Brij35 (N-term)">Brij35 (N-term)</option> <option value="Brij58 (N-term)">Brij58 (N-term)</option> <option value="Bromo (F)">Bromo (F)</option> @@ -3697,9 +3738,9 @@ <option value="Dehydrated (T)">Dehydrated (T)</option> <option value="Dehydrated (Y)">Dehydrated (Y)</option> <option value="Dehydro (C)">Dehydro (C)</option> + <option value="Delta:H(-1)N(-1)18O(1) (N)">Delta:H(-1)N(-1)18O(1) (N)</option> <option value="Delta:H(-4)O(2) (W)">Delta:H(-4)O(2) (W)</option> <option value="Delta:H(-4)O(3) (W)">Delta:H(-4)O(3) (W)</option> - <option value="Delta:H(1)N(-1)18O(1) (N)">Delta:H(1)N(-1)18O(1) (N)</option> <option value="Delta:H(10)C(8)O(1) (K)">Delta:H(10)C(8)O(1) (K)</option> <option value="Delta:H(2)C(2) (H)">Delta:H(2)C(2) (H)</option> <option value="Delta:H(2)C(2) (K)">Delta:H(2)C(2) (K)</option> @@ -3709,7 +3750,6 @@ <option value="Delta:H(2)C(3)O(1) (K)">Delta:H(2)C(3)O(1) (K)</option> <option value="Delta:H(2)C(3)O(1) (R)">Delta:H(2)C(3)O(1) (R)</option> <option value="Delta:H(2)C(5) (K)">Delta:H(2)C(5) (K)</option> - <option value="Delta:H(3)C(3)O(2) (K)">Delta:H(3)C(3)O(2) (K)</option> <option value="Delta:H(4)C(2) (H)">Delta:H(4)C(2) (H)</option> <option value="Delta:H(4)C(2) (K)">Delta:H(4)C(2) (K)</option> <option value="Delta:H(4)C(2) (N-term)">Delta:H(4)C(2) (N-term)</option> @@ -3721,6 +3761,7 @@ <option value="Delta:H(4)C(3)O(1) (H)">Delta:H(4)C(3)O(1) (H)</option> <option value="Delta:H(4)C(3)O(1) (K)">Delta:H(4)C(3)O(1) (K)</option> <option value="Delta:H(4)C(3)O(1) (R)">Delta:H(4)C(3)O(1) (R)</option> + <option value="Delta:H(4)C(3)O(2) (K)">Delta:H(4)C(3)O(2) (K)</option> <option value="Delta:H(4)C(5)O(1) (R)">Delta:H(4)C(5)O(1) (R)</option> <option value="Delta:H(4)C(6) (K)">Delta:H(4)C(6) (K)</option> <option value="Delta:H(5)C(2) (P)">Delta:H(5)C(2) (P)</option> @@ -4293,7 +4334,6 @@ <option value="Ethanolyl (C)">Ethanolyl (C)</option> <option value="Ethanolyl (K)">Ethanolyl (K)</option> <option value="Ethanolyl (R)">Ethanolyl (R)</option> - <option value="Ethoxyformyl (H)">Ethoxyformyl (H)</option> <option value="Ethyl (C-term)">Ethyl (C-term)</option> <option value="Ethyl (D)">Ethyl (D)</option> <option value="Ethyl (E)">Ethyl (E)</option> @@ -4387,6 +4427,7 @@ <option value="Gln->Xle (Q)">Gln->Xle (Q)</option> <option value="Glu (E)">Glu (E)</option> <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> + <option value="Glu+O(2) (H)">Glu+O(2) (H)</option> <option value="Glu->Ala (E)">Glu->Ala (E)</option> <option value="Glu->Arg (E)">Glu->Arg (E)</option> <option value="Glu->Asn (E)">Glu->Asn (E)</option> @@ -4401,7 +4442,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> <option value="Glu->Thr (E)">Glu->Thr (E)</option> @@ -4425,6 +4465,7 @@ <option value="Gly (K)">Gly (K)</option> <option value="Gly (S)">Gly (S)</option> <option value="Gly (T)">Gly (T)</option> + <option value="Gly+O(2) (H)">Gly+O(2) (H)</option> <option value="Gly->Ala (G)">Gly->Ala (G)</option> <option value="Gly->Arg (G)">Gly->Arg (G)</option> <option value="Gly->Asn (G)">Gly->Asn (G)</option> @@ -4815,6 +4856,7 @@ <option value="Hex(6)HexNAc(4)Me(3) (N)">Hex(6)HexNAc(4)Me(3) (N)</option> <option value="Hex(6)HexNAc(4)Me(3)Pent(1) (N)">Hex(6)HexNAc(4)Me(3)Pent(1) (N)</option> <option value="Hex(6)HexNAc(5) (N)">Hex(6)HexNAc(5) (N)</option> + <option value="Hex(6)HexNAc(5)NeuAc(3) (N)">Hex(6)HexNAc(5)NeuAc(3) (N)</option> <option value="Hex(6)Phos(1) (S)">Hex(6)Phos(1) (S)</option> <option value="Hex(6)Phos(1) (T)">Hex(6)Phos(1) (T)</option> <option value="Hex(6)Phos(3) (S)">Hex(6)Phos(3) (S)</option> @@ -4826,6 +4868,9 @@ <option value="Hex(7)HexNAc(3) (N)">Hex(7)HexNAc(3) (N)</option> <option value="Hex(7)HexNAc(3)Phos(1) (N)">Hex(7)HexNAc(3)Phos(1) (N)</option> <option value="Hex(7)HexNAc(4) (N)">Hex(7)HexNAc(4) (N)</option> + <option value="Hex(7)HexNAc(6) (N)">Hex(7)HexNAc(6) (N)</option> + <option value="Hex(7)HexNAc(6) (S)">Hex(7)HexNAc(6) (S)</option> + <option value="Hex(7)HexNAc(6) (T)">Hex(7)HexNAc(6) (T)</option> <option value="Hex(7)Phos(3) (S)">Hex(7)Phos(3) (S)</option> <option value="Hex(7)Phos(3) (T)">Hex(7)Phos(3) (T)</option> <option value="Hex(8)HexNAc(1) (N)">Hex(8)HexNAc(1) (N)</option> @@ -4881,6 +4926,7 @@ <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> + <option value="His+O(2) (H)">His+O(2) (H)</option> <option value="His->Ala (H)">His->Ala (H)</option> <option value="His->Arg (H)">His->Arg (H)</option> <option value="His->Asn (H)">His->Asn (H)</option> @@ -5018,11 +5064,14 @@ <option value="iTRAQ8plex:13C(6)15N(2) (K)">iTRAQ8plex:13C(6)15N(2) (K)</option> <option value="iTRAQ8plex:13C(6)15N(2) (N-term)">iTRAQ8plex:13C(6)15N(2) (N-term)</option> <option value="iTRAQ8plex:13C(6)15N(2) (Y)">iTRAQ8plex:13C(6)15N(2) (Y)</option> + <option value="Kdo (S)">Kdo (S)</option> + <option value="Kdo (T)">Kdo (T)</option> <option value="Label:13C(1)2H(3) (M)">Label:13C(1)2H(3) (M)</option> <option value="Label:13C(1)2H(3)+Oxidation (M)">Label:13C(1)2H(3)+Oxidation (M)</option> <option value="Label:13C(2)15N(2) (K)">Label:13C(2)15N(2) (K)</option> <option value="Label:13C(3) (A)">Label:13C(3) (A)</option> <option value="Label:13C(3)15N(1) (A)">Label:13C(3)15N(1) (A)</option> + <option value="Label:13C(3)15N(1) (S)">Label:13C(3)15N(1) (S)</option> <option value="Label:13C(4) (M)">Label:13C(4) (M)</option> <option value="Label:13C(4)+Oxidation (M)">Label:13C(4)+Oxidation (M)</option> <option value="Label:13C(4)15N(1) (D)">Label:13C(4)15N(1) (D)</option> @@ -5107,13 +5156,16 @@ <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> + <option value="LG-pyrrole (C)">LG-pyrrole (C)</option> <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> <option value="Lipoyl (K)">Lipoyl (K)</option> <option value="LRGG (K)">LRGG (K)</option> <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> + <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option> <option value="Lys (N-term)">Lys (N-term)</option> + <option value="Lys+O(2) (H)">Lys+O(2) (H)</option> <option value="Lys->Ala (K)">Lys->Ala (K)</option> <option value="Lys->Allysine (K)">Lys->Allysine (K)</option> <option value="Lys->AminoadipicAcid (K)">Lys->AminoadipicAcid (K)</option> @@ -5148,6 +5200,7 @@ <option value="Malonyl (C)">Malonyl (C)</option> <option value="Malonyl (K)">Malonyl (K)</option> <option value="Malonyl (S)">Malonyl (S)</option> + <option value="MBS+peptide (C)">MBS+peptide (C)</option> <option value="MDCC (C)">MDCC (C)</option> <option value="MeMePhosphorothioate (S)">MeMePhosphorothioate (S)</option> <option value="Menadione (C)">Menadione (C)</option> @@ -5159,6 +5212,7 @@ <option value="MesitylOxide (H)">MesitylOxide (H)</option> <option value="MesitylOxide (K)">MesitylOxide (K)</option> <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> + <option value="Met+O(2) (H)">Met+O(2) (H)</option> <option value="Met->Aha (M)">Met->Aha (M)</option> <option value="Met->Ala (M)">Met->Ala (M)</option> <option value="Met->Arg (M)">Met->Arg (M)</option> @@ -5342,7 +5396,6 @@ <option value="Nmethylmaleimide+water (C)">Nmethylmaleimide+water (C)</option> <option value="NO_SMX_SEMD (C)">NO_SMX_SEMD (C)</option> <option value="NO_SMX_SIMD (C)">NO_SMX_SIMD (C)</option> - <option value="NO_SMX_SMCT (C)">NO_SMX_SMCT (C)</option> <option value="NP40 (N-term)">NP40 (N-term)</option> <option value="NQIGG (K)">NQIGG (K)</option> <option value="O-Dimethylphosphate (S)">O-Dimethylphosphate (S)</option> @@ -5430,6 +5483,10 @@ <option value="Phe->Tyr (F)">Phe->Tyr (F)</option> <option value="Phe->Val (F)">Phe->Val (F)</option> <option value="Phe->Xle (F)">Phe->Xle (F)</option> + <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option> + <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option> + <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option> + <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option> <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> @@ -5444,6 +5501,7 @@ <option value="Phospho (Y)">Phospho (Y)</option> <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> + <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option> <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> @@ -5475,6 +5533,7 @@ <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> <option value="Piperidine (K)">Piperidine (K)</option> <option value="Piperidine (N-term)">Piperidine (N-term)</option> + <option value="Pro+O(2) (H)">Pro+O(2) (H)</option> <option value="Pro->Ala (P)">Pro->Ala (P)</option> <option value="Pro->Arg (P)">Pro->Arg (P)</option> <option value="Pro->Asn (P)">Pro->Asn (P)</option> @@ -5552,18 +5611,30 @@ <option value="QTGG (K)">QTGG (K)</option> <option value="Quinone (W)">Quinone (W)</option> <option value="Quinone (Y)">Quinone (Y)</option> + <option value="RBS-ID_Uridine (A)">RBS-ID_Uridine (A)</option> + <option value="RBS-ID_Uridine (C)">RBS-ID_Uridine (C)</option> + <option value="RBS-ID_Uridine (D)">RBS-ID_Uridine (D)</option> + <option value="RBS-ID_Uridine (E)">RBS-ID_Uridine (E)</option> + <option value="RBS-ID_Uridine (F)">RBS-ID_Uridine (F)</option> + <option value="RBS-ID_Uridine (G)">RBS-ID_Uridine (G)</option> + <option value="RBS-ID_Uridine (H)">RBS-ID_Uridine (H)</option> + <option value="RBS-ID_Uridine (I)">RBS-ID_Uridine (I)</option> + <option value="RBS-ID_Uridine (K)">RBS-ID_Uridine (K)</option> + <option value="RBS-ID_Uridine (L)">RBS-ID_Uridine (L)</option> + <option value="RBS-ID_Uridine (M)">RBS-ID_Uridine (M)</option> + <option value="RBS-ID_Uridine (N)">RBS-ID_Uridine (N)</option> + <option value="RBS-ID_Uridine (P)">RBS-ID_Uridine (P)</option> + <option value="RBS-ID_Uridine (Q)">RBS-ID_Uridine (Q)</option> + <option value="RBS-ID_Uridine (R)">RBS-ID_Uridine (R)</option> + <option value="RBS-ID_Uridine (S)">RBS-ID_Uridine (S)</option> + <option value="RBS-ID_Uridine (T)">RBS-ID_Uridine (T)</option> + <option value="RBS-ID_Uridine (V)">RBS-ID_Uridine (V)</option> + <option value="RBS-ID_Uridine (W)">RBS-ID_Uridine (W)</option> + <option value="RBS-ID_Uridine (Y)">RBS-ID_Uridine (Y)</option> <option value="Retinylidene (K)">Retinylidene (K)</option> <option value="RNPXL (N-term K)">RNPXL (N-term K)</option> <option value="RNPXL (N-term R)">RNPXL (N-term R)</option> <option value="RNPXlink1 (C)">RNPXlink1 (C)</option> - <option value="RNPXlink2 (F)">RNPXlink2 (F)</option> - <option value="RNPXlink2 (K)">RNPXlink2 (K)</option> - <option value="RNPXlink2 (L)">RNPXlink2 (L)</option> - <option value="RNPXlink3 (C)">RNPXlink3 (C)</option> - <option value="RNPXlink3 (F)">RNPXlink3 (F)</option> - <option value="RNPXlink4 (C)">RNPXlink4 (C)</option> - <option value="RNPXlink5 (F)">RNPXlink5 (F)</option> - <option value="RNPXlink5 (Y)">RNPXlink5 (Y)</option> <option value="s-GlcNAc (S)">s-GlcNAc (S)</option> <option value="s-GlcNAc (T)">s-GlcNAc (T)</option> <option value="Saligenin (H)">Saligenin (H)</option> @@ -5591,6 +5662,9 @@ <option value="shTMT (K)">shTMT (K)</option> <option value="shTMT (N-term)">shTMT (N-term)</option> <option value="shTMT (Protein N-term)">shTMT (Protein N-term)</option> + <option value="shTMTpro (K)">shTMTpro (K)</option> + <option value="shTMTpro (N-term)">shTMTpro (N-term)</option> + <option value="shTMTpro (Protein N-term)">shTMTpro (Protein N-term)</option> <option value="SMA (K)">SMA (K)</option> <option value="SMA (N-term)">SMA (N-term)</option> <option value="spermidine (Q)">spermidine (Q)</option> @@ -5766,7 +5840,6 @@ <option value="Tyr->Trp (Y)">Tyr->Trp (Y)</option> <option value="Tyr->Val (Y)">Tyr->Val (Y)</option> <option value="Tyr->Xle (Y)">Tyr->Xle (Y)</option> - <option value="Ub-amide (C)">Ub-amide (C)</option> <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> <option value="Ub-VME (C)">Ub-VME (C)</option> @@ -5961,11 +6034,11 @@ <option value="ZQG (K)">ZQG (K)</option> <expand macro="list_string_san" name="variable"/> </param> - <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> + <param name="variable_max_per_peptide" argument="-modifications:variable_max_per_peptide" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate peptide" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -5981,7 +6054,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_SpecLibSearcher_1 --> + <tests> + <!-- TOPP_SpecLibSearcher_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -6013,8 +6087,6 @@ <param name="cut_peaks_below" value="1000"/> </section> <section name="modifications"> - <param name="fixed"/> - <param name="variable"/> <param name="variable_max_per_peptide" value="2"/> </section> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> @@ -6023,11 +6095,14 @@ <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpecLibSearcher.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpecLibSearcher.html]]></help> <expand macro="references"/> </tool>