Mercurial > repos > galaxyp > openms_rnpxlsearch
diff RNPxlSearch.xml @ 12:33e2670c3a18 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 21:44:45 +0000 |
| parents | 0f97ea098da0 |
| children |
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--- a/RNPxlSearch.xml Thu Dec 01 19:19:49 2022 +0000 +++ b/RNPxlSearch.xml Fri Jun 14 21:44:45 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: [Utilities]--> +<!--Proposed Tool Section: [Cross-Linking]--> <tool id="RNPxlSearch" name="RNPxlSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra.</description> + <description>Annotate RNA/DNA-peptide cross-links in MS/MS spectra</description> <macros> <token name="@EXECUTABLE@">RNPxlSearch</token> <import>macros.xml</import> @@ -15,9 +14,9 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir database && -ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && +cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && mkdir out && #if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir out_tsv && @@ -56,31 +55,31 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> - <param argument="-database" type="data" format="fasta" optional="false" label="input file" help=" select fasta data sets(s)"/> + <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/> + <param argument="-database" type="data" format="fasta" label="input file" help=" select fasta data sets(s)"/> <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="Precursor mass tolerance (+/- around precursor m/z)" 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="Precursor mass tolerance (+/- around precursor m/z)" 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 (+/- around fragment m/z)" help=""/> - <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment m" help=""> + <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> + <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment m" help=""> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> <expand macro="list_string_san" name="mass_tolerance_unit"/> </param> </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> @@ -90,6 +89,10 @@ <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> @@ -179,6 +182,7 @@ <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> @@ -282,6 +286,7 @@ <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> @@ -314,7 +319,6 @@ <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> @@ -746,9 +750,9 @@ <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> @@ -758,7 +762,6 @@ <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> @@ -770,6 +773,7 @@ <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> @@ -1342,7 +1346,6 @@ <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> @@ -1436,6 +1439,7 @@ <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> @@ -1450,7 +1454,6 @@ <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> @@ -1474,6 +1477,7 @@ <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> @@ -1864,6 +1868,7 @@ <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> @@ -1875,6 +1880,9 @@ <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> @@ -1930,6 +1938,7 @@ <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> @@ -2067,11 +2076,14 @@ <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> @@ -2156,13 +2168,16 @@ <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> @@ -2197,6 +2212,7 @@ <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> @@ -2208,6 +2224,7 @@ <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> @@ -2391,7 +2408,6 @@ <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> @@ -2479,6 +2495,10 @@ <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> @@ -2493,6 +2513,7 @@ <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> @@ -2524,6 +2545,7 @@ <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> @@ -2601,18 +2623,30 @@ <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> @@ -2640,6 +2674,9 @@ <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> @@ -2815,7 +2852,6 @@ <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> @@ -3010,7 +3046,7 @@ <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> @@ -3020,6 +3056,10 @@ <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> @@ -3109,6 +3149,7 @@ <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> @@ -3212,6 +3253,7 @@ <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> @@ -3244,7 +3286,6 @@ <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> @@ -3676,9 +3717,9 @@ <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> @@ -3688,7 +3729,6 @@ <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> @@ -3700,6 +3740,7 @@ <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> @@ -4272,7 +4313,6 @@ <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> @@ -4366,6 +4406,7 @@ <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> @@ -4380,7 +4421,6 @@ <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> @@ -4404,6 +4444,7 @@ <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> @@ -4794,6 +4835,7 @@ <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> @@ -4805,6 +4847,9 @@ <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> @@ -4860,6 +4905,7 @@ <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> @@ -4997,11 +5043,14 @@ <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> @@ -5086,13 +5135,16 @@ <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> @@ -5127,6 +5179,7 @@ <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> @@ -5138,6 +5191,7 @@ <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> @@ -5321,7 +5375,6 @@ <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> @@ -5409,6 +5462,10 @@ <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> @@ -5423,6 +5480,7 @@ <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> @@ -5454,6 +5512,7 @@ <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> @@ -5531,18 +5590,30 @@ <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> @@ -5570,6 +5641,9 @@ <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> @@ -5745,7 +5819,6 @@ <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> @@ -5940,58 +6013,58 @@ <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> <section name="peptide" title="Peptide Options" help="" expanded="false"> - <param name="min_size" argument="-peptide:min_size" type="integer" optional="true" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> - <param name="max_size" argument="-peptide:max_size" type="integer" optional="true" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/> - <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> - <param name="enzyme" argument="-peptide:enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help=""> + <param name="min_size" argument="-peptide:min_size" type="integer" value="6" label="Minimum size a peptide must have after digestion to be considered in the search" help=""/> + <param name="max_size" argument="-peptide:max_size" type="integer" value="1000000" label="Maximum size a peptide may have after digestion to be considered in the search" help=""/> + <param name="missed_cleavages" argument="-peptide:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/> + <param name="enzyme" argument="-peptide:enzyme" type="select" label="The enzyme used for peptide digestion" help=""> + <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> + <option value="Alpha-lytic protease">Alpha-lytic protease</option> + <option value="2-iodobenzoate">2-iodobenzoate</option> + <option value="iodosobenzoate">iodosobenzoate</option> + <option value="Lys-C/P">Lys-C/P</option> <option value="PepsinA">PepsinA</option> - <option value="TrypChymo">TrypChymo</option> - <option value="Trypsin/P">Trypsin/P</option> <option value="Trypsin" selected="true">Trypsin</option> - <option value="Lys-N">Lys-N</option> - <option value="Lys-C/P">Lys-C/P</option> - <option value="Clostripain/P">Clostripain/P</option> - <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> - <option value="no cleavage">no cleavage</option> - <option value="unspecific cleavage">unspecific cleavage</option> - <option value="Arg-C/P">Arg-C/P</option> - <option value="Asp-N">Asp-N</option> - <option value="Asp-N/B">Asp-N/B</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Chymotrypsin/P">Chymotrypsin/P</option> + <option value="CNBr">CNBr</option> <option value="staphylococcal protease/D">staphylococcal protease/D</option> <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option> <option value="Glu-C+P">Glu-C+P</option> <option value="PepsinA + P">PepsinA + P</option> <option value="cyanogen-bromide">cyanogen-bromide</option> - <option value="Asp-N_ambic">Asp-N_ambic</option> - <option value="Chymotrypsin">Chymotrypsin</option> - <option value="Chymotrypsin/P">Chymotrypsin/P</option> - <option value="Arg-C">Arg-C</option> - <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> - <option value="Alpha-lytic protease">Alpha-lytic protease</option> - <option value="2-iodobenzoate">2-iodobenzoate</option> - <option value="iodosobenzoate">iodosobenzoate</option> - <option value="CNBr">CNBr</option> <option value="Formic_acid">Formic_acid</option> <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Arg-C">Arg-C</option> + <option value="Arg-C/P">Arg-C/P</option> <option value="V8-DE">V8-DE</option> <option value="V8-E">V8-E</option> + <option value="Asp-N">Asp-N</option> + <option value="Asp-N/B">Asp-N/B</option> + <option value="Asp-N_ambic">Asp-N_ambic</option> <option value="leukocyte elastase">leukocyte elastase</option> <option value="proline endopeptidase">proline endopeptidase</option> + <option value="TrypChymo">TrypChymo</option> + <option value="Trypsin/P">Trypsin/P</option> + <option value="Clostripain/P">Clostripain/P</option> + <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option> + <option value="no cleavage">no cleavage</option> + <option value="unspecific cleavage">unspecific cleavage</option> <expand macro="list_string_san" name="enzyme"/> </param> </section> <section name="report" title="Reporting Options" help="" expanded="false"> - <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> + <param name="top_hits" argument="-report:top_hits" type="integer" value="1" label="Maximum number of top scoring hits per spectrum that are reported" help=""/> </section> <section name="RNPxl" title="RNPxl Options" help="" expanded="false"> - <param name="length" argument="-RNPxl:length" type="integer" optional="true" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/> + <param name="length" argument="-RNPxl:length" type="integer" value="2" label="Oligonucleotide maximum length" help="0 = disable search for RNA variants"/> <param name="sequence" argument="-RNPxl:sequence" type="text" optional="true" value="" label="Sequence to restrict the generation of oligonucleotide chains" help="(disabled for empty sequence)"> <expand macro="list_string_san" name="sequence"/> </param> - <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" optional="true" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="target_nucleotides" argument="-RNPxl:target_nucleotides" type="text" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU . or e.g. Y=C10H14N5O7PS where Y represents tG (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="target_nucleotides"/> <expand macro="list_string_san" name="target_nucleotides"/> </param> @@ -5999,22 +6072,22 @@ <expand macro="list_string_val" name="nt_groups"/> <expand macro="list_string_san" name="nt_groups"/> </param> - <param name="mapping" argument="-RNPxl:mapping" type="text" optional="true" value="A->A C->C G->G U->U" label="format: source->target e.g. A->A, ..., U->U, U->X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="mapping" argument="-RNPxl:mapping" type="text" value="A->A C->C G->G U->U" label="format: source->target e.g. A->A, ..., U->U, U->X" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="mapping"/> <expand macro="list_string_san" name="mapping"/> </param> - <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" optional="true" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links"> + <param name="can_cross_link" argument="-RNPxl:can_cross_link" type="text" value="U" label="format: 'U' if only U forms cross-links" help="'CATG' if C, A, G, and T form cross-links"> <expand macro="list_string_san" name="can_cross_link"/> </param> - <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" optional="true" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]->[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O->C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="fragment_adducts" argument="-RNPxl:fragment_adducts" type="text" value="U:C9H10N2O5;U-H3PO4 U:C4H4N2O2;U' U:C4H2N2O1;U'-H2O U:C3O;C3O U:C9H13N2O9P1;U U:C9H11N2O8P1;U-H2O U:C9H12N2O6;U-HPO3" label="format: [target nucleotide]:[formula] or [precursor adduct]->[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O->C9H11N2O8P1;U-H2O', (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="fragment_adducts"/> <expand macro="list_string_san" name="fragment_adducts"/> </param> - <param name="modifications" argument="-RNPxl:modifications" type="text" optional="true" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param name="modifications" argument="-RNPxl:modifications" type="text" value="U: U:-H2O U:-H2O-HPO3 U:-HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="modifications"/> <expand macro="list_string_san" name="modifications"/> </param> - <param name="scoring" argument="-RNPxl:scoring" type="select" optional="true" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help=""> + <param name="scoring" argument="-RNPxl:scoring" type="select" label="Scoring algorithm used in prescoring (fast: total-loss, slow: all losses)" help=""> <option value="fast" selected="true">fast</option> <option value="slow">slow</option> <expand macro="list_string_san" name="scoring"/> @@ -6024,12 +6097,12 @@ <param name="filter_fractional_mass" argument="-RNPxl:filter_fractional_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag to filter non-crosslinks by fractional mass" help=""/> <param name="carbon_labeled_fragments" argument="-RNPxl:carbon_labeled_fragments" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate fragment shifts assuming full labeling of carbon" help="(e.g. completely labeled U13)"/> <param name="only_xl" argument="-RNPxl:only_xl" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only search cross-links and ignore non-cross-linked peptides" help=""/> - <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" optional="true" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/> - <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" help=""/> + <param name="filter_small_peptide_mass" argument="-RNPxl:filter_small_peptide_mass" type="float" value="600.0" label="Filter precursor that can only correspond to non-crosslinks by mass" help=""/> + <param name="marker_ions_tolerance" argument="-RNPxl:marker_ions_tolerance" type="float" value="0.05" label="Tolerance used to determine marker ions (Da)" 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> @@ -6047,7 +6120,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_RNPxlSearch_1 --> + <tests> + <!-- TOPP_RNPxlSearch_1 --> <test expect_num_outputs="2"> <section name="adv_opts"> <param name="force" value="false"/> @@ -6055,7 +6129,7 @@ </section> <param name="in" value="RNPxlSearch_1_input.mzML"/> <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="out" value="RNPxlSearch_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> <section name="precursor"> <param name="mass_tolerance" value="20.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -6068,7 +6142,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed"/> <param name="variable" value="Oxidation (M)"/> <param name="variable_max_per_peptide" value="2"/> </section> @@ -6085,7 +6158,6 @@ <param name="length" value="2"/> <param name="sequence" value="GUA"/> <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> <param name="can_cross_link" value="U"/> <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> @@ -6105,6 +6177,9 @@ <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> <!-- TOPP_RNPxlSearch_2 --> <test expect_num_outputs="2"> @@ -6114,7 +6189,7 @@ </section> <param name="in" value="RNPxlSearch_1_input.mzML"/> <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="out" value="RNPxlSearch_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> <section name="precursor"> <param name="mass_tolerance" value="20.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -6127,7 +6202,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed"/> <param name="variable" value="Oxidation (M)"/> <param name="variable_max_per_peptide" value="2"/> </section> @@ -6144,7 +6218,6 @@ <param name="length" value="2"/> <param name="sequence" value="GUA"/> <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> <param name="can_cross_link" value="U"/> <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> @@ -6164,6 +6237,9 @@ <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> <!-- TOPP_RNPxlSearch_3 --> <test expect_num_outputs="3"> @@ -6173,8 +6249,8 @@ </section> <param name="in" value="RNPxlSearch_1_input.mzML"/> <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="RNPxlSearch_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="out_tsv" value="RNPxlSearch_3_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <section name="precursor"> <param name="mass_tolerance" value="10.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -6187,8 +6263,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed"/> - <param name="variable"/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -6204,7 +6278,6 @@ <param name="length" value="2"/> <param name="sequence" value=""/> <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> <param name="can_cross_link" value="U"/> <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> @@ -6224,6 +6297,9 @@ <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> <!-- TOPP_RNPxlSearch_4 --> <test expect_num_outputs="3"> @@ -6233,8 +6309,8 @@ </section> <param name="in" value="RNPxlSearch_1_input.mzML"/> <param name="database" value="RNPxlSearch_1_input.fasta"/> - <output name="out" file="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> - <output name="out_tsv" file="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> + <output name="out" value="RNPxlSearch_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <output name="out_tsv" value="RNPxlSearch_4_output2.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/> <section name="precursor"> <param name="mass_tolerance" value="10.0"/> <param name="mass_tolerance_unit" value="ppm"/> @@ -6247,8 +6323,6 @@ <param name="mass_tolerance_unit" value="ppm"/> </section> <section name="modifications"> - <param name="fixed"/> - <param name="variable"/> <param name="variable_max_per_peptide" value="2"/> </section> <section name="peptide"> @@ -6264,7 +6338,6 @@ <param name="length" value="2"/> <param name="sequence" value=""/> <param name="target_nucleotides" value=""A=C10H14N5O7P" "C=C9H14N3O8P" "G=C10H14N5O8P" "U=C9H13N2O9P""/> - <param name="nt_groups" value=""/> <param name="mapping" value=""A->A" "C->C" "G->G" "U->U""/> <param name="can_cross_link" value="U"/> <param name="fragment_adducts" value=""U:C9H10N2O5;U-H3PO4" "U:C4H4N2O2;U'" "U:C4H2N2O1;U'-H2O" "U:C3O;C3O" "U:C9H13N2O9P1;U" "U:C9H11N2O8P1;U-H2O" "U:C9H12N2O6;U-HPO3""/> @@ -6284,11 +6357,14 @@ <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[Annotate RNA/DNA-peptide cross-links in MS/MS spectra. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlSearch.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNPxlSearch.html]]></help> <expand macro="references"/> </tool>