Mercurial > repos > galaxyp > openms_staticmodification
diff StaticModification.xml @ 3:ace4851c8c37 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 21:46:23 +0000 |
| parents | 9989f6be8bea |
| children |
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--- a/StaticModification.xml Thu Dec 01 19:15:09 2022 +0000 +++ b/StaticModification.xml Fri Jun 14 21:46:23 2024 +0000 @@ -1,8 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> -<!--Proposed Tool Section: [Utilities]--> +<!--Proposed Tool Section: [Identification Processing]--> <tool id="StaticModification" name="StaticModification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Applies a set of modifications to all PeptideIDs in an idXML file.</description> + <description>Applies a set of modifications to all PeptideIDs in an idXML file</description> <macros> <token name="@EXECUTABLE@">StaticModification</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## 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 out && ## Main program call @@ -39,8 +38,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="idxml" optional="false" label="Input: identification results" help=" select idxml data sets(s)"/> - <param argument="-mods" multiple="true" type="select" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'"> + <param argument="-in" type="data" format="idxml" label="Input: identification results" help=" select idxml data sets(s)"/> + <param argument="-mods" type="select" multiple="true" optional="true" label="List of manual modifications, specified using Unimod (www.unimod.org) terms" help="e.g. 'Carbamidomethyl (C)' or '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> @@ -50,6 +49,10 @@ <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> @@ -139,6 +142,7 @@ <option value="AMTzHexNAc2 (N)">AMTzHexNAc2 (N)</option> <option value="AMTzHexNAc2 (S)">AMTzHexNAc2 (S)</option> <option value="AMTzHexNAc2 (T)">AMTzHexNAc2 (T)</option> + <option value="Andro-H2O (C)">Andro-H2O (C)</option> <option value="Archaeol (C)">Archaeol (C)</option> <option value="Arg (N-term)">Arg (N-term)</option> <option value="Arg->Ala (R)">Arg->Ala (R)</option> @@ -242,6 +246,7 @@ <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> @@ -274,7 +279,6 @@ <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> @@ -706,9 +710,9 @@ <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> @@ -718,7 +722,6 @@ <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> @@ -730,6 +733,7 @@ <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> @@ -1302,7 +1306,6 @@ <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> @@ -1396,6 +1399,7 @@ <option value="Gln->Xle (Q)">Gln->Xle (Q)</option> <option value="Glu (E)">Glu (E)</option> <option value="Glu (Protein C-term)">Glu (Protein C-term)</option> + <option value="Glu+O(2) (H)">Glu+O(2) (H)</option> <option value="Glu->Ala (E)">Glu->Ala (E)</option> <option value="Glu->Arg (E)">Glu->Arg (E)</option> <option value="Glu->Asn (E)">Glu->Asn (E)</option> @@ -1410,7 +1414,6 @@ <option value="Glu->Pro (E)">Glu->Pro (E)</option> <option value="Glu->pyro-Glu (N-term E)">Glu->pyro-Glu (N-term E)</option> <option value="Glu->pyro-Glu+Methyl (N-term E)">Glu->pyro-Glu+Methyl (N-term E)</option> - <option value="Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C (N-term E)</option> <option value="Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)">Glu->pyro-Glu+Methyl:2H(2)13C(1) (N-term E)</option> <option value="Glu->Ser (E)">Glu->Ser (E)</option> <option value="Glu->Thr (E)">Glu->Thr (E)</option> @@ -1434,6 +1437,7 @@ <option value="Gly (K)">Gly (K)</option> <option value="Gly (S)">Gly (S)</option> <option value="Gly (T)">Gly (T)</option> + <option value="Gly+O(2) (H)">Gly+O(2) (H)</option> <option value="Gly->Ala (G)">Gly->Ala (G)</option> <option value="Gly->Arg (G)">Gly->Arg (G)</option> <option value="Gly->Asn (G)">Gly->Asn (G)</option> @@ -1824,6 +1828,7 @@ <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> @@ -1835,6 +1840,9 @@ <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> @@ -1890,6 +1898,7 @@ <option value="HexNAc(4) (T)">HexNAc(4) (T)</option> <option value="HexNAc(5) (S)">HexNAc(5) (S)</option> <option value="HexNAc(5) (T)">HexNAc(5) (T)</option> + <option value="His+O(2) (H)">His+O(2) (H)</option> <option value="His->Ala (H)">His->Ala (H)</option> <option value="His->Arg (H)">His->Arg (H)</option> <option value="His->Asn (H)">His->Asn (H)</option> @@ -2027,11 +2036,14 @@ <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> @@ -2116,13 +2128,16 @@ <option value="LG-lactam-K (K)">LG-lactam-K (K)</option> <option value="LG-lactam-K (Protein N-term)">LG-lactam-K (Protein N-term)</option> <option value="LG-lactam-R (R)">LG-lactam-R (R)</option> + <option value="LG-pyrrole (C)">LG-pyrrole (C)</option> <option value="LG-pyrrole (K)">LG-pyrrole (K)</option> <option value="LG-pyrrole (N-term)">LG-pyrrole (N-term)</option> <option value="Lipoyl (K)">Lipoyl (K)</option> <option value="LRGG (K)">LRGG (K)</option> <option value="LRGG+dimethyl (K)">LRGG+dimethyl (K)</option> <option value="LRGG+methyl (K)">LRGG+methyl (K)</option> + <option value="LTX+Lophotoxin (Y)">LTX+Lophotoxin (Y)</option> <option value="Lys (N-term)">Lys (N-term)</option> + <option value="Lys+O(2) (H)">Lys+O(2) (H)</option> <option value="Lys->Ala (K)">Lys->Ala (K)</option> <option value="Lys->Allysine (K)">Lys->Allysine (K)</option> <option value="Lys->AminoadipicAcid (K)">Lys->AminoadipicAcid (K)</option> @@ -2157,6 +2172,7 @@ <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> @@ -2168,6 +2184,7 @@ <option value="MesitylOxide (H)">MesitylOxide (H)</option> <option value="MesitylOxide (K)">MesitylOxide (K)</option> <option value="MesitylOxide (Protein N-term)">MesitylOxide (Protein N-term)</option> + <option value="Met+O(2) (H)">Met+O(2) (H)</option> <option value="Met->Aha (M)">Met->Aha (M)</option> <option value="Met->Ala (M)">Met->Ala (M)</option> <option value="Met->Arg (M)">Met->Arg (M)</option> @@ -2351,7 +2368,6 @@ <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> @@ -2439,6 +2455,10 @@ <option value="Phe->Tyr (F)">Phe->Tyr (F)</option> <option value="Phe->Val (F)">Phe->Val (F)</option> <option value="Phe->Xle (F)">Phe->Xle (F)</option> + <option value="phenyl-phosphate (K)">phenyl-phosphate (K)</option> + <option value="phenyl-phosphate (S)">phenyl-phosphate (S)</option> + <option value="phenyl-phosphate (T)">phenyl-phosphate (T)</option> + <option value="phenyl-phosphate (Y)">phenyl-phosphate (Y)</option> <option value="Phenylisocyanate (N-term)">Phenylisocyanate (N-term)</option> <option value="Phenylisocyanate:2H(5) (N-term)">Phenylisocyanate:2H(5) (N-term)</option> <option value="phenylsulfonylethyl (C)">phenylsulfonylethyl (C)</option> @@ -2453,6 +2473,7 @@ <option value="Phospho (Y)">Phospho (Y)</option> <option value="Phosphoadenosine (H)">Phosphoadenosine (H)</option> <option value="Phosphoadenosine (K)">Phosphoadenosine (K)</option> + <option value="Phosphoadenosine (S)">Phosphoadenosine (S)</option> <option value="Phosphoadenosine (T)">Phosphoadenosine (T)</option> <option value="Phosphoadenosine (Y)">Phosphoadenosine (Y)</option> <option value="PhosphoCytidine (S)">PhosphoCytidine (S)</option> @@ -2484,6 +2505,7 @@ <option value="Phytochromobilin (C)">Phytochromobilin (C)</option> <option value="Piperidine (K)">Piperidine (K)</option> <option value="Piperidine (N-term)">Piperidine (N-term)</option> + <option value="Pro+O(2) (H)">Pro+O(2) (H)</option> <option value="Pro->Ala (P)">Pro->Ala (P)</option> <option value="Pro->Arg (P)">Pro->Arg (P)</option> <option value="Pro->Asn (P)">Pro->Asn (P)</option> @@ -2561,18 +2583,30 @@ <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> @@ -2600,6 +2634,9 @@ <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> @@ -2775,7 +2812,6 @@ <option value="Tyr->Trp (Y)">Tyr->Trp (Y)</option> <option value="Tyr->Val (Y)">Tyr->Val (Y)</option> <option value="Tyr->Xle (Y)">Tyr->Xle (Y)</option> - <option value="Ub-amide (C)">Ub-amide (C)</option> <option value="Ub-Br2 (C)">Ub-Br2 (C)</option> <option value="Ub-fluorescein (C)">Ub-fluorescein (C)</option> <option value="Ub-VME (C)">Ub-VME (C)</option> @@ -2970,14 +3006,14 @@ <option value="ZQG (K)">ZQG (K)</option> <expand macro="list_string_san" name="mods"/> </param> - <param argument="-presets" type="select" optional="true" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help=""> + <param argument="-presets" type="select" label="Add predefined sets, as shortcut to manually specifying a lot of modifications" help=""> <option value="none" selected="true">none</option> <option value="N15">N15</option> <expand macro="list_string_san" name="presets"/> </param> <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> @@ -2995,6 +3031,6 @@ <help><![CDATA[Applies a set of modifications to all PeptideIDs in an idXML file. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_StaticModification.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_StaticModification.html]]></help> <expand macro="references"/> </tool>