diff LuciphorAdapter.xml @ 15:949086930a49 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 21:39:41 +0000
parents bf2bf60c8af2
children
line wrap: on
line diff
--- a/LuciphorAdapter.xml	Thu Dec 01 19:03:21 2022 +0000
+++ b/LuciphorAdapter.xml	Fri Jun 14 21:39:41 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: [ID Processing]-->
+<!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
 <tool id="LuciphorAdapter" name="LuciphorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Modification site localisation using LuciPHOr2.</description>
+  <description>Modification site localisation using LuciPHOr2</description>
   <macros>
     <token name="@EXECUTABLE@">LuciphorAdapter</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($in.ext)' &&
 mkdir id &&
-ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
+cp '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
 mkdir out &&
 
 ## Main program call
@@ -43,21 +42,21 @@
     <configfile name="hardcoded_json"><![CDATA[{"executable": "\$(dirname \$(realpath \$(which luciphor2)))/luciphor2.jar", "num_threads": "\${GALAXY_SLOTS:-1}", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input spectrum file" help=" select mzml data sets(s)"/>
-    <param argument="-id" type="data" format="idxml" optional="false" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
-    <param argument="-fragment_method" type="select" optional="true" label="Fragmentation method" help="">
+    <param argument="-in" type="data" format="mzml" label="Input spectrum file" help=" select mzml data sets(s)"/>
+    <param argument="-id" type="data" format="idxml" label="Protein/peptide identifications file" help=" select idxml data sets(s)"/>
+    <param argument="-fragment_method" type="select" label="Fragmentation method" help="">
       <option value="CID" selected="true">CID</option>
       <option value="HCD">HCD</option>
       <expand macro="list_string_san" name="fragment_method"/>
     </param>
-    <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
-    <param argument="-fragment_error_units" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
+    <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Tolerance of the peaks in the fragment spectrum" help=""/>
+    <param argument="-fragment_error_units" type="select" label="Unit of fragment mass tolerance" help="">
       <option value="Da" selected="true">Da</option>
       <option value="ppm">ppm</option>
       <expand macro="list_string_san" name="fragment_error_units"/>
     </param>
-    <param argument="-min_mz" type="float" optional="true" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
-    <param argument="-target_modifications" multiple="true" type="select" optional="true" label="List the amino acids to be searched for and their mass modifications, specified using UniMod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)'">
+    <param argument="-min_mz" type="float" value="150.0" label="Do not consider peaks below this value for matching fragment ions" help=""/>
+    <param argument="-target_modifications" type="select" multiple="true" optional="false" label="List the amino acids to be searched for and their mass 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>
@@ -67,6 +66,10 @@
       <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>
@@ -156,6 +159,7 @@
       <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-&gt;Ala (R)">Arg-&gt;Ala (R)</option>
@@ -259,6 +263,7 @@
       <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>
@@ -291,7 +296,6 @@
       <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>
@@ -723,9 +727,9 @@
       <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>
@@ -735,7 +739,6 @@
       <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>
@@ -747,6 +750,7 @@
       <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>
@@ -1319,7 +1323,6 @@
       <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>
@@ -1413,6 +1416,7 @@
       <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>
@@ -1427,7 +1431,6 @@
       <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>
@@ -1451,6 +1454,7 @@
       <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-&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>
@@ -1841,6 +1845,7 @@
       <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>
@@ -1852,6 +1857,9 @@
       <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>
@@ -1907,6 +1915,7 @@
       <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-&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>
@@ -2044,11 +2053,14 @@
       <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>
@@ -2133,13 +2145,16 @@
       <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-&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>
@@ -2174,6 +2189,7 @@
       <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>
@@ -2185,6 +2201,7 @@
       <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-&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>
@@ -2368,7 +2385,6 @@
       <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>
@@ -2456,6 +2472,10 @@
       <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>
@@ -2470,6 +2490,7 @@
       <option value="Phospho (Y)" selected="true">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>
@@ -2501,6 +2522,7 @@
       <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-&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>
@@ -2578,18 +2600,30 @@
       <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>
@@ -2617,6 +2651,9 @@
       <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>
@@ -2792,7 +2829,6 @@
       <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>
@@ -2987,30 +3023,30 @@
       <option value="ZQG (K)">ZQG (K)</option>
       <expand macro="list_string_san" name="target_modifications"/>
     </param>
-    <param argument="-neutral_losses" type="text" optional="true" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-neutral_losses" type="text" value="&quot;sty -H3PO4 -97.97690&quot;" label="List the types of neutral losses that you want to conside" help="The residue field is case sensitive. For example: lower case 'sty' implies that the neutral loss can only occur if the specified modification is present. Syntax: NL = &lt;RESDIUES&gt; -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="neutral_losses"/>
       <expand macro="list_string_san" name="neutral_losses"/>
     </param>
-    <param argument="-decoy_mass" type="float" optional="true" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
-    <param argument="-decoy_neutral_losses" type="text" optional="true" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
+    <param argument="-decoy_mass" type="float" min="1.0" value="79.966331" label="How much to add to an amino acid to make it a decoy" help=""/>
+    <param argument="-decoy_neutral_losses" type="text" value="&quot;X -H3PO4 -97.97690&quot;" label="For handling the neutral loss from a decoy sequence" help="The syntax for this is identical to that of the normal neutral losses given above except that the residue is always 'X'. Syntax: DECOY_NL = X -&lt;NEUTRAL_LOSS_MOLECULAR_FORMULA&gt; &lt;MASS_LOST&gt; (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="decoy_neutral_losses"/>
       <expand macro="list_string_san" name="decoy_neutral_losses"/>
     </param>
-    <param argument="-max_charge_state" type="integer" optional="true" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
-    <param argument="-max_peptide_length" type="integer" optional="true" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
-    <param argument="-max_num_perm" type="integer" optional="true" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
-    <param argument="-modeling_score_threshold" type="float" optional="true" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
-    <param argument="-scoring_threshold" type="float" optional="true" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
-    <param argument="-min_num_psms_model" type="integer" optional="true" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
-    <param argument="-run_mode" type="select" optional="true" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
+    <param argument="-max_charge_state" type="integer" min="1" value="5" label="Do not consider PSMs with a charge state above this value" help=""/>
+    <param argument="-max_peptide_length" type="integer" min="1" value="40" label="Restrict scoring to peptides with a length shorter than this value" help=""/>
+    <param argument="-max_num_perm" type="integer" min="1" value="16384" label="Maximum number of permutations a sequence can have" help=""/>
+    <param argument="-modeling_score_threshold" type="float" min="0.0" value="0.95" label="Minimum score a PSM needs to be considered for modeling" help=""/>
+    <param argument="-scoring_threshold" type="float" min="0.0" value="0.0" label="PSMs below this value will be discarded" help=""/>
+    <param argument="-min_num_psms_model" type="integer" min="1" value="50" label="The minimum number of PSMs you need for any charge state in order to build a model for it" help=""/>
+    <param argument="-run_mode" type="select" label="Determines how Luciphor will run: 0 = calculate FLR then rerun scoring without decoys (two iterations), 1 = Report Decoys: calculate FLR but don't rescore PSMs, all decoy hits will be reported" help="">
       <option value="0" selected="true">0</option>
       <option value="1">1</option>
       <expand macro="list_string_san" name="run_mode"/>
     </param>
-    <param argument="-rt_tolerance" type="float" optional="true" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
+    <param argument="-rt_tolerance" type="float" min="0.0" value="0.01" label="Set the retention time tolerance (for the mapping of identifications to spectra in case multiple search engines were used)" help=""/>
     <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>
@@ -3024,7 +3060,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_LuciphorAdapter_1 -->
+  <tests>
+    <!-- TOPP_LuciphorAdapter_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -3032,7 +3069,7 @@
       </section>
       <param name="in" value="LuciphorAdapter_1_input.mzML"/>
       <param name="id" value="LuciphorAdapter_1_input.idXML"/>
-      <output name="out" file="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="LuciphorAdapter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="fragment_method" value="CID"/>
       <param name="fragment_mass_tolerance" value="0.5"/>
       <param name="fragment_error_units" value="Da"/>
@@ -3055,11 +3092,14 @@
           <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[Modification site localisation using LuciPHOr2.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_LuciphorAdapter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_LuciphorAdapter.html]]></help>
   <expand macro="references"/>
 </tool>