openms_rnpxlsearch: RNPxlSearch.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:0f97ea098da0
+:33e2670c3a18
-<?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>
 </macros>
 <expand macro="requirements"/>
 @EXT_FOO@
 #import re
 ## 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 &&
 #end if
 <configfiles>
 <inputs name="args_json" data_style="paths"/>
 <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="-in" type="data" format="mzml" 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="-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" 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" optional="true" label="Unit of precursor mass tolerance" 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="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" optional="true" value="5" label="Maximum 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" 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="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" 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" optional="true" label="Unit of fragment m" 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>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
 <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>
 <option value="4-ONE (H)">4-ONE (H)</option>
 <option value="4-ONE (K)">4-ONE (K)</option>
 <option value="Ammonium (D)">Ammonium (D)</option>
 <option value="Ammonium (E)">Ammonium (E)</option>
 <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-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
 <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>
 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
 <option value="BITC (C)">BITC (C)</option>
 <option value="BITC (K)">BITC (K)</option>
 <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>
 <option value="Bromo (H)">Bromo (H)</option>
 <option value="Bromo (W)">Bromo (W)</option>
 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
 <option value="Dehydrated (S)">Dehydrated (S)</option>
 <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>
 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
 <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>
 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
 <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>
 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
 <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>
 <option value="Ethyl (K)">Ethyl (K)</option>
 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
 <option value="Gln-&gt;Xle (Q)">Gln-&gt;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-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-<option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
 <option value="Gluratylation (K)">Gluratylation (K)</option>
 <option value="Glutathione (C)">Glutathione (C)</option>
 <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-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
 <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>
 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
 <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>
 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
 <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-&gt;Ala (H)">His-&gt;Ala (H)</option>
 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
 <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>
 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
 <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-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
 <option value="maleimide5 (C)">maleimide5 (C)</option>
 <option value="maleimide5 (K)">maleimide5 (K)</option>
 <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>
 <option value="Menadione (K)">Menadione (K)</option>
 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
 <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-&gt;Aha (M)">Met-&gt;Aha (M)</option>
 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
 <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>
 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
 <option value="Phe-&gt;Xle (F)">Phe-&gt;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>
 <option value="Phospho (C)">Phospho (C)</option>
 <option value="Phospho (D)">Phospho (D)</option>
 <option value="Phospho (S)">Phospho (S)</option>
 <option value="Phospho (T)">Phospho (T)</option>
 <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>
 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
 <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-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
 <option value="QEQTGG (K)">QEQTGG (K)</option>
 <option value="QQQTGG (K)">QQQTGG (K)</option>
 <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>
 <option value="Saligenin (K)">Saligenin (K)</option>
 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
 <option value="serotonylation (Q)">serotonylation (Q)</option>
 <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>
 <option value="spermine (Q)">spermine (Q)</option>
 <option value="SPITC (K)">SPITC (K)</option>
 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;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>
 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
 <option value="ZGB (K)">ZGB (K)</option>
 <option value="ZGB (N-term)">ZGB (N-term)</option>
 <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>
 <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
 <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
 <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>
 <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>
 <option value="4-ONE (H)">4-ONE (H)</option>
 <option value="4-ONE (K)">4-ONE (K)</option>
 <option value="Ammonium (D)">Ammonium (D)</option>
 <option value="Ammonium (E)">Ammonium (E)</option>
 <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-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
 <option value="Arg-&gt;Asn (R)">Arg-&gt;Asn (R)</option>
 <option value="Arg-&gt;Asp (R)">Arg-&gt;Asp (R)</option>
 <option value="Biotin-PEO-Amine (Protein C-term)">Biotin-PEO-Amine (Protein C-term)</option>
 <option value="Biotin-phenacyl (C)">Biotin-phenacyl (C)</option>
 <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>
 <option value="Biotin:Sigma-B1267 (C)">Biotin:Sigma-B1267 (C)</option>
 <option value="Biotin:Thermo-21325 (K)">Biotin:Thermo-21325 (K)</option>
 <option value="BITC (C)">BITC (C)</option>
 <option value="BITC (K)">BITC (K)</option>
 <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>
 <option value="Bromo (H)">Bromo (H)</option>
 <option value="Bromo (W)">Bromo (W)</option>
 <option value="Dehydrated (Protein C-term Q)">Dehydrated (Protein C-term Q)</option>
 <option value="Dehydrated (S)">Dehydrated (S)</option>
 <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>
 <option value="Delta:H(2)C(2) (N-term)">Delta:H(2)C(2) (N-term)</option>
 <option value="Delta:H(2)C(2) (Protein N-term)">Delta:H(2)C(2) (Protein N-term)</option>
 <option value="Delta:H(2)C(3) (K)">Delta:H(2)C(3) (K)</option>
 <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>
 <option value="Delta:H(4)C(2)O(-1)S(1) (S)">Delta:H(4)C(2)O(-1)S(1) (S)</option>
 <option value="Delta:H(4)C(3) (H)">Delta:H(4)C(3) (H)</option>
 <option value="Delta:H(4)C(3) (Protein N-term)">Delta:H(4)C(3) (Protein N-term)</option>
 <option value="Delta:H(4)C(3)O(1) (C)">Delta:H(4)C(3)O(1) (C)</option>
 <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>
 <option value="Delta:H(6)C(3)O(1) (C)">Delta:H(6)C(3)O(1) (C)</option>
 <option value="Delta:H(6)C(3)O(1) (H)">Delta:H(6)C(3)O(1) (H)</option>
 <option value="Ethanolamine (D)">Ethanolamine (D)</option>
 <option value="Ethanolamine (E)">Ethanolamine (E)</option>
 <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>
 <option value="Ethyl (K)">Ethyl (K)</option>
 <option value="Ethyl (N-term)">Ethyl (N-term)</option>
 <option value="Gln-&gt;Tyr (Q)">Gln-&gt;Tyr (Q)</option>
 <option value="Gln-&gt;Val (Q)">Gln-&gt;Val (Q)</option>
 <option value="Gln-&gt;Xle (Q)">Gln-&gt;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-&gt;Ala (E)">Glu-&gt;Ala (E)</option>
 <option value="Glu-&gt;Arg (E)">Glu-&gt;Arg (E)</option>
 <option value="Glu-&gt;Asn (E)">Glu-&gt;Asn (E)</option>
 <option value="Glu-&gt;Asp (E)">Glu-&gt;Asp (E)</option>
 <option value="Glu-&gt;Cys (E)">Glu-&gt;Cys (E)</option>
 <option value="Glu-&gt;Met (E)">Glu-&gt;Met (E)</option>
 <option value="Glu-&gt;Phe (E)">Glu-&gt;Phe (E)</option>
 <option value="Glu-&gt;Pro (E)">Glu-&gt;Pro (E)</option>
 <option value="Glu-&gt;pyro-Glu (N-term E)">Glu-&gt;pyro-Glu (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl (N-term E)">Glu-&gt;pyro-Glu+Methyl (N-term E)</option>
-<option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C (N-term E)</option>
 <option value="Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu-&gt;pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option>
 <option value="Glu-&gt;Ser (E)">Glu-&gt;Ser (E)</option>
 <option value="Glu-&gt;Thr (E)">Glu-&gt;Thr (E)</option>
 <option value="Glu-&gt;Trp (E)">Glu-&gt;Trp (E)</option>
 <option value="Glu-&gt;Tyr (E)">Glu-&gt;Tyr (E)</option>
 <option value="Gluratylation (K)">Gluratylation (K)</option>
 <option value="Glutathione (C)">Glutathione (C)</option>
 <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-&gt;Ala (G)">Gly-&gt;Ala (G)</option>
 <option value="Gly-&gt;Arg (G)">Gly-&gt;Arg (G)</option>
 <option value="Gly-&gt;Asn (G)">Gly-&gt;Asn (G)</option>
 <option value="Gly-&gt;Asp (G)">Gly-&gt;Asp (G)</option>
 <option value="Gly-&gt;Cys (G)">Gly-&gt;Cys (G)</option>
 <option value="Hex(6)HexNAc(4) (S)">Hex(6)HexNAc(4) (S)</option>
 <option value="Hex(6)HexNAc(4) (T)">Hex(6)HexNAc(4) (T)</option>
 <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>
 <option value="Hex(6)Phos(3) (T)">Hex(6)Phos(3) (T)</option>
 <option value="Hex(7)HexNAc(1) (N)">Hex(7)HexNAc(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(1) (N)">Hex(7)HexNAc(2)Phos(1) (N)</option>
 <option value="Hex(7)HexNAc(2)Phos(2) (N)">Hex(7)HexNAc(2)Phos(2) (N)</option>
 <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>
 <option value="Hex(8)HexNAc(2) (N)">Hex(8)HexNAc(2) (N)</option>
 <option value="Hex(8)Phos(3) (S)">Hex(8)Phos(3) (S)</option>
 <option value="HexNAc(3)Sulf(1) (T)">HexNAc(3)Sulf(1) (T)</option>
 <option value="HexNAc(4) (S)">HexNAc(4) (S)</option>
 <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-&gt;Ala (H)">His-&gt;Ala (H)</option>
 <option value="His-&gt;Arg (H)">His-&gt;Arg (H)</option>
 <option value="His-&gt;Asn (H)">His-&gt;Asn (H)</option>
 <option value="His-&gt;Asp (H)">His-&gt;Asp (H)</option>
 <option value="His-&gt;Cys (H)">His-&gt;Cys (H)</option>
 <option value="iTRAQ8plex (Y)">iTRAQ8plex (Y)</option>
 <option value="iTRAQ8plex:13C(6)15N(2) (C)">iTRAQ8plex:13C(6)15N(2) (C)</option>
 <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>
 <option value="Label:13C(4)15N(2)+GG (K)">Label:13C(4)15N(2)+GG (K)</option>
 <option value="Label:13C(5) (P)">Label:13C(5) (P)</option>
 <option value="LG-Hlactam-K (Protein N-term)">LG-Hlactam-K (Protein N-term)</option>
 <option value="LG-Hlactam-R (R)">LG-Hlactam-R (R)</option>
 <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-&gt;Ala (K)">Lys-&gt;Ala (K)</option>
 <option value="Lys-&gt;Allysine (K)">Lys-&gt;Allysine (K)</option>
 <option value="Lys-&gt;AminoadipicAcid (K)">Lys-&gt;AminoadipicAcid (K)</option>
 <option value="Lys-&gt;Arg (K)">Lys-&gt;Arg (K)</option>
 <option value="Lys-&gt;Asn (K)">Lys-&gt;Asn (K)</option>
 <option value="maleimide5 (C)">maleimide5 (C)</option>
 <option value="maleimide5 (K)">maleimide5 (K)</option>
 <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>
 <option value="Menadione (K)">Menadione (K)</option>
 <option value="Menadione-HQ (C)">Menadione-HQ (C)</option>
 <option value="MercaptoEthanol (S)">MercaptoEthanol (S)</option>
 <option value="MercaptoEthanol (T)">MercaptoEthanol (T)</option>
 <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-&gt;Aha (M)">Met-&gt;Aha (M)</option>
 <option value="Met-&gt;Ala (M)">Met-&gt;Ala (M)</option>
 <option value="Met-&gt;Arg (M)">Met-&gt;Arg (M)</option>
 <option value="Met-&gt;Asn (M)">Met-&gt;Asn (M)</option>
 <option value="Met-&gt;Asp (M)">Met-&gt;Asp (M)</option>
 <option value="Nmethylmaleimide (C)">Nmethylmaleimide (C)</option>
 <option value="Nmethylmaleimide (K)">Nmethylmaleimide (K)</option>
 <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>
 <option value="O-Dimethylphosphate (T)">O-Dimethylphosphate (T)</option>
 <option value="O-Dimethylphosphate (Y)">O-Dimethylphosphate (Y)</option>
 <option value="Phe-&gt;Thr (F)">Phe-&gt;Thr (F)</option>
 <option value="Phe-&gt;Trp (F)">Phe-&gt;Trp (F)</option>
 <option value="Phe-&gt;Tyr (F)">Phe-&gt;Tyr (F)</option>
 <option value="Phe-&gt;Val (F)">Phe-&gt;Val (F)</option>
 <option value="Phe-&gt;Xle (F)">Phe-&gt;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>
 <option value="Phospho (C)">Phospho (C)</option>
 <option value="Phospho (D)">Phospho (D)</option>
 <option value="Phospho (S)">Phospho (S)</option>
 <option value="Phospho (T)">Phospho (T)</option>
 <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>
 <option value="PhosphoCytidine (T)">PhosphoCytidine (T)</option>
 <option value="PhosphoCytidine (Y)">PhosphoCytidine (Y)</option>
 <option value="Phycocyanobilin (C)">Phycocyanobilin (C)</option>
 <option value="Phycoerythrobilin (C)">Phycoerythrobilin (C)</option>
 <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-&gt;Ala (P)">Pro-&gt;Ala (P)</option>
 <option value="Pro-&gt;Arg (P)">Pro-&gt;Arg (P)</option>
 <option value="Pro-&gt;Asn (P)">Pro-&gt;Asn (P)</option>
 <option value="Pro-&gt;Asp (P)">Pro-&gt;Asp (P)</option>
 <option value="Pro-&gt;Cys (P)">Pro-&gt;Cys (P)</option>
 <option value="QEQTGG (K)">QEQTGG (K)</option>
 <option value="QQQTGG (K)">QQQTGG (K)</option>
 <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>
 <option value="Saligenin (K)">Saligenin (K)</option>
 <option value="Ser-&gt;Ala (S)">Ser-&gt;Ala (S)</option>
 <option value="Ser-&gt;Xle (S)">Ser-&gt;Xle (S)</option>
 <option value="serotonylation (Q)">serotonylation (Q)</option>
 <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>
 <option value="spermine (Q)">spermine (Q)</option>
 <option value="SPITC (K)">SPITC (K)</option>
 <option value="Tyr-&gt;Ser (Y)">Tyr-&gt;Ser (Y)</option>
 <option value="Tyr-&gt;Thr (Y)">Tyr-&gt;Thr (Y)</option>
 <option value="Tyr-&gt;Trp (Y)">Tyr-&gt;Trp (Y)</option>
 <option value="Tyr-&gt;Val (Y)">Tyr-&gt;Val (Y)</option>
 <option value="Tyr-&gt;Xle (Y)">Tyr-&gt;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>
 <option value="UgiJoullie (D)">UgiJoullie (D)</option>
 <option value="UgiJoullie (E)">UgiJoullie (E)</option>
 <option value="ZGB (K)">ZGB (K)</option>
 <option value="ZGB (N-term)">ZGB (N-term)</option>
 <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="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" optional="true" value="1000000" label="Maximum size a peptide may 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" optional="true" value="1" label="Number of missed cleavages" 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" optional="true" label="The enzyme used for peptide digestion" 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="Chymotrypsin">Chymotrypsin</option>
-<option value="Lys-C/P">Lys-C/P</option>
+<option value="Chymotrypsin/P">Chymotrypsin/P</option>
-<option value="Clostripain/P">Clostripain/P</option>
+<option value="CNBr">CNBr</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="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>
 <param name="nt_groups" argument="-RNPxl:nt_groups" type="text" optional="true" value="" label="Restrict which nucleotides can cooccur in a precursor adduct to be able to search both RNA and DNA (Formate" help="e.g.: AU CG) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
 <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-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;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-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;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]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;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]-&gt;[fragment adduct formula];[name]:" help="e.g., 'U:C9H10N2O5;U-H3PO4' or 'U:U-H2O-&gt;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"/>
 </param>
 <param name="decoys" argument="-RNPxl:decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate decoy sequences and spectra" help=""/>
 <param name="CysteineAdduct" argument="-RNPxl:CysteineAdduct" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the +152 adduct is expected" help=""/>
 <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="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" optional="true" value="0.05" label="Tolerance used to determine marker ions (Da)" 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>
 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
 <option value="out_tsv_FLAG">out_tsv (tsv output file)</option>
 </data>
 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
 <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"/>
 <param name="test" value="true"/>
 </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"/>
 <param name="min_charge" value="2"/>
 <param name="max_charge" value="5"/>
 <section name="fragment">
 <param name="mass_tolerance" value="20.0"/>
 <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>
 <section name="peptide">
 <param name="min_size" value="6"/>
 </section>
 <section name="RNPxl">
 <param name="length" value="2"/>
 <param name="sequence" value="GUA"/>
 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-<param name="nt_groups" value=""/>
 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
 <param name="can_cross_link" value="U"/>
 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
 <param name="scoring" value="fast"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <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">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </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"/>
 <param name="min_charge" value="2"/>
 <param name="max_charge" value="5"/>
 <section name="fragment">
 <param name="mass_tolerance" value="20.0"/>
 <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>
 <section name="peptide">
 <param name="min_size" value="6"/>
 </section>
 <section name="RNPxl">
 <param name="length" value="2"/>
 <param name="sequence" value="GUA"/>
 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-<param name="nt_groups" value=""/>
 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
 <param name="can_cross_link" value="U"/>
 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
 <param name="scoring" value="fast"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <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">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </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" value="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_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"/>
 <param name="min_charge" value="2"/>
 <param name="max_charge" value="5"/>
 <section name="fragment">
 <param name="mass_tolerance" value="10.0"/>
 <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">
 <param name="min_size" value="6"/>
 <param name="max_size" value="1000000"/>
 </section>
 <section name="RNPxl">
 <param name="length" value="2"/>
 <param name="sequence" value=""/>
 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-<param name="nt_groups" value=""/>
 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
 <param name="can_cross_link" value="U"/>
 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
 <param name="scoring" value="fast"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <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">
 <section name="adv_opts">
 <param name="force" value="false"/>
 <param name="test" value="true"/>
 </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" value="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_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"/>
 <param name="min_charge" value="2"/>
 <param name="max_charge" value="5"/>
 <section name="fragment">
 <param name="mass_tolerance" value="10.0"/>
 <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">
 <param name="min_size" value="6"/>
 <param name="max_size" value="1000000"/>
 </section>
 <section name="RNPxl">
 <param name="length" value="2"/>
 <param name="sequence" value=""/>
 <param name="target_nucleotides" value="&quot;A=C10H14N5O7P&quot; &quot;C=C9H14N3O8P&quot; &quot;G=C10H14N5O8P&quot; &quot;U=C9H13N2O9P&quot;"/>
-<param name="nt_groups" value=""/>
 <param name="mapping" value="&quot;A-&gt;A&quot; &quot;C-&gt;C&quot; &quot;G-&gt;G&quot; &quot;U-&gt;U&quot;"/>
 <param name="can_cross_link" value="U"/>
 <param name="fragment_adducts" value="&quot;U:C9H10N2O5;U-H3PO4&quot; &quot;U:C4H4N2O2;U'&quot; &quot;U:C4H2N2O1;U'-H2O&quot; &quot;U:C3O;C3O&quot; &quot;U:C9H13N2O9P1;U&quot; &quot;U:C9H11N2O8P1;U-H2O&quot; &quot;U:C9H12N2O6;U-HPO3&quot;"/>
 <param name="modifications" value="&quot;U:&quot; &quot;U:-H2O&quot; &quot;U:-H2O-HPO3&quot; &quot;U:-HPO3&quot;"/>
 <param name="scoring" value="fast"/>
 <output name="ctd_out" ftype="xml">
 <assert_contents>
 <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>

Mercurial > repos > galaxyp > openms_rnpxlsearch

comparison RNPxlSearch.xml @ 12:33e2670c3a18 draft default tip