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Updated MSMetaEnhancer to 0.4.0 #512

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merged 2 commits into from
Apr 16, 2024
Merged

Updated MSMetaEnhancer to 0.4.0 #512

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40796d2
updated msmetaenhancer to 0.4.0
zargham-ahmad Mar 26, 2024
deaf577
Merge branch 'master' into issue501
hechth Apr 16, 2024
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14 changes: 13 additions & 1 deletion tools/msmetaenhancer/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">0.3.0</token>
<token name="@TOOL_VERSION@">0.4.0</token>

<xml name="creator">
<creator>
Expand Down Expand Up @@ -40,6 +40,7 @@

<xml name="job_options">
<option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option>
<option value="formula mw RDKit">RDKit: formula -> mw</option>
<option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option>
<option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option>
<option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option>
Expand Down Expand Up @@ -82,8 +83,19 @@
<option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
<option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
<option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option>
<option value="inchikey canonical_smiles PubChem">PubChem: inchikey -> canonical_smiles</option>
<option value="inchikey formula PubChem">PubChem: inchikey -> formula</option>
<option value="inchikey inchi PubChem">PubChem: inchikey -> inchi</option>
<option value="inchikey isomeric_smiles PubChem">PubChem: inchikey -> isomeric_smiles</option>
<option value="inchikey iupac_name PubChem">PubChem: inchikey -> iupac_name</option>
<option value="inchikey pubchemid PubChem">PubChem: inchikey -> pubchemid</option>
<option value="pubchemid canonical_smiles PubChem">PubChem: pubchemid -> canonical_smiles</option>
<option value="pubchemid formula PubChem">PubChem: pubchemid -> formula</option>
<option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option>
<option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option>
<option value="pubchemid inchikey PubChem">PubChem: pubchemid -> inchikey</option>
<option value="pubchemid isomeric_smiles PubChem">PubChem: pubchemid -> isomeric_smiles</option>
<option value="pubchemid iupac_name PubChem">PubChem: pubchemid -> iupac_name</option>
<option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option>
<option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option>
<option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option>
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2 changes: 1 addition & 1 deletion tools/msmetaenhancer/msmetaenhancer.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy3">
<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
<description>annotate MS data</description>

<macros>
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12 changes: 6 additions & 6 deletions tools/msmetaenhancer/test-data/sample_out.msp
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Original file line number Diff line number Diff line change
@@ -1,33 +1,33 @@
FORMULA: H2
MW: 2
CASNO: 1333-74-0
ID: 1
COMMENT: NIST MS# 245692, Seq# M1
COMPOUND_NAME: Hydrogen
NOMINAL_MASS: 2
INCHI: InChI=1S/H2/h1H
CANONICAL_SMILES: [HH]
NUM PEAKS: 2
1.0 20.98
2.0 999.0

FORMULA: D2
MW: 4
CASNO: 7782-39-0
ID: 2
COMMENT: NIST MS# 61316, Seq# M2
COMPOUND_NAME: Deuterium
NOMINAL_MASS: 4
INCHI: InChI=1S/H2/h1H/i1+1D
CANONICAL_SMILES: [HH]
NUM PEAKS: 2
2.0 14.99
4.0 999.0

FORMULA: CH4
MW: 16
CASNO: 74-82-8
ID: 3
COMMENT: Any=100 ; NIST MS# 61313, Seq# M64
COMPOUND_NAME: Methane
NOMINAL_MASS: 16
INCHI: InChI=1S/CH4/h1H4
CANONICAL_SMILES: C
NUM PEAKS: 6
Expand All @@ -39,11 +39,11 @@ NUM PEAKS: 6
17.0 15.99

FORMULA: CH4
MW: 16
CASNO: 74-82-8
ID: 4
COMMENT: Any=100 ; NIST MS# 18807, Seq# R26
COMPOUND_NAME: Methane
NOMINAL_MASS: 16
INCHI: InChI=1S/CH4/h1H4
CANONICAL_SMILES: C
NUM PEAKS: 6
Expand All @@ -55,11 +55,11 @@ NUM PEAKS: 6
17.0 10.99

FORMULA: CH4
MW: 16
CASNO: 74-82-8
ID: 5
COMMENT: Any=100 ; NIST MS# 18809, Seq# R27
COMPOUND_NAME: Methane
NOMINAL_MASS: 16
INCHI: InChI=1S/CH4/h1H4
CANONICAL_SMILES: C
NUM PEAKS: 6
Expand All @@ -71,11 +71,11 @@ NUM PEAKS: 6
17.0 11.99

FORMULA: CH4
MW: 16
CASNO: 74-82-8
ID: 6
COMMENT: Any=100 ; NIST MS# 423924, Seq# R28
COMPOUND_NAME: Methane
NOMINAL_MASS: 16
INCHI: InChI=1S/CH4/h1H4
CANONICAL_SMILES: C
NUM PEAKS: 6
Expand Down
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