Mercurial > repos > recetox > msmetaenhancer

changeset 11:791bf4d9b06c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
author recetox
date Tue, 16 Apr 2024 11:23:32 +0000
parents 3e2cb0bc6959
children a6af1e124e06
files macros.xml msmetaenhancer.xml msmetaenhancer_wrapper.py test-data/sample_out.msp
diffstat 4 files changed, 25 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Oct 12 13:30:31 2023 +0000
+++ b/macros.xml	Tue Apr 16 11:23:32 2024 +0000
@@ -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>
@@ -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>
@@ -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>
--- a/msmetaenhancer.xml	Thu Oct 12 13:30:31 2023 +0000
+++ b/msmetaenhancer.xml	Tue Apr 16 11:23:32 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy3">
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0"  profile="21.09">
     <description>annotate MS data</description>
 
     <macros>
@@ -84,7 +84,7 @@
             <change_format>
                 <when input="input_file.ext" value="mgf" format="mgf" />
                 <when input="input_file.ext" value="json" format="json" />
-                <when input="input_file.ext" value="csv" format="csv" />
+                <when input="input_file.ext" value="csv" format="tsv" />
                 <when input="input_file.ext" value="tsv" format="tsv" />
                 <when input="input_file.ext" value="xlsx" format="xlsx" />
             </change_format>
--- a/msmetaenhancer_wrapper.py	Thu Oct 12 13:30:31 2023 +0000
+++ b/msmetaenhancer_wrapper.py	Tue Apr 16 11:23:32 2024 +0000
@@ -56,7 +56,10 @@
     if args.file_format == 'xlsx':
         handle_xlsx_file(app, args.output_file)
     else:
-        app.save_data(args.output_file, file_format=args.file_format)
+        if args.file_format == 'csv':
+            app.save_data(args.output_file, file_format="tsv")
+        else:
+            app.save_data(args.output_file, file_format=args.file_format)
     return 0
 
 
--- a/test-data/sample_out.msp	Thu Oct 12 13:30:31 2023 +0000
+++ b/test-data/sample_out.msp	Tue Apr 16 11:23:32 2024 +0000
@@ -1,9 +1,9 @@
 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
@@ -11,11 +11,11 @@
 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
@@ -23,11 +23,11 @@
 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
@@ -39,11 +39,11 @@
 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
@@ -55,11 +55,11 @@
 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
@@ -71,11 +71,11 @@
 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