Mercurial > repos > recetox > msmetaenhancer

changeset 3:b48c57453a25 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
author recetox
date Tue, 22 Mar 2022 15:33:04 +0000
parents 4ae5b466a805
children e329be622dc8
files macros.xml msmetaenhancer.xml msmetaenhancer_wrapper.py test-data/sample_out.msp
diffstat 4 files changed, 68 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Feb 15 12:26:04 2022 +0000
+++ b/macros.xml	Tue Mar 22 15:33:04 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.3</token>
+    <token name="@TOOL_VERSION@">0.2.0</token>
 
     <xml name="creator">
         <creator>
@@ -32,22 +32,28 @@
     </token>
 
     <xml name="job_options">
-        <option value="inchi canonical_smiles PubChem">PubChem: inchi -> canonical_smiles</option>
-        <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
-        <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
-        <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
-        <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
-        <option value="name canonical_smiles PubChem">PubChem: name -> canonical_smiles</option>
-        <option value="name formula PubChem">PubChem: name -> formula</option>
-        <option value="name inchi PubChem">PubChem: name -> inchi</option>
-        <option value="name inchikey PubChem">PubChem: name -> inchikey</option>
-        <option value="name isomeric_smiles PubChem">PubChem: name -> isomeric_smiles</option>
-        <option value="name iupac_name PubChem">PubChem: name -> iupac_name</option>
+        <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option>
+        <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option>
+        <option value="smiles mw RDKit">RDKit: smiles -> mw</option>
+        <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option>
+        <option value="compound_name formula IDSM">IDSM: compound_name -> formula</option>
+        <option value="compound_name inchi IDSM">IDSM: compound_name -> inchi</option>
+        <option value="compound_name inchikey IDSM">IDSM: compound_name -> inchikey</option>
+        <option value="compound_name isomeric_smiles IDSM">IDSM: compound_name -> isomeric_smiles</option>
+        <option value="compound_name iupac_name IDSM">IDSM: compound_name -> iupac_name</option>
+        <option value="inchi canonical_smiles IDSM">IDSM: inchi -> canonical_smiles</option>
+        <option value="inchi formula IDSM">IDSM: inchi -> formula</option>
+        <option value="inchi inchikey IDSM">IDSM: inchi -> inchikey</option>
+        <option value="inchi isomeric_smiles IDSM">IDSM: inchi -> isomeric_smiles</option>
+        <option value="inchi iupac_name IDSM">IDSM: inchi -> iupac_name</option>
+        <option value="iupac_name inchi IDSM">IDSM: iupac_name -> inchi</option>
+        <option value="casno inchi CTS">CTS: casno -> inchi</option>
         <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
+        <option value="compound_name inchikey CTS">CTS: compound_name -> inchikey</option>
+        <option value="hmdbid inchi CTS">CTS: hmdbid -> inchi</option>
+        <option value="inchikey compound_name CTS">CTS: inchikey -> compound_name</option>
         <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
         <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
-        <option value="inchikey name CTS">CTS: inchikey -> name</option>
-        <option value="name inchikey CTS">CTS: name -> inchikey</option>
         <option value="casno smiles CIR">CIR: casno -> smiles</option>
         <option value="inchi smiles CIR">CIR: inchi -> smiles</option>
         <option value="inchikey casno CIR">CIR: inchikey -> casno</option>
@@ -55,12 +61,46 @@
         <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option>
         <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option>
         <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option>
+        <option value="compound_name casno NLM">NLM: compound_name -> casno</option>
+        <option value="compound_name formula NLM">NLM: compound_name -> formula</option>
+        <option value="compound_name inchikey NLM">NLM: compound_name -> inchikey</option>
         <option value="inchikey casno NLM">NLM: inchikey -> casno</option>
+        <option value="inchikey compound_name NLM">NLM: inchikey -> compound_name</option>
         <option value="inchikey formula NLM">NLM: inchikey -> formula</option>
-        <option value="inchikey name NLM">NLM: inchikey -> name</option>
-        <option value="name casno NLM">NLM: name -> casno</option>
-        <option value="name formula NLM">NLM: name -> formula</option>
-        <option value="name inchikey NLM">NLM: name -> inchikey</option>
+        <option value="compound_name canonical_smiles PubChem">PubChem: compound_name -> canonical_smiles</option>
+        <option value="compound_name formula PubChem">PubChem: compound_name -> formula</option>
+        <option value="compound_name inchi PubChem">PubChem: compound_name -> inchi</option>
+        <option value="compound_name inchikey PubChem">PubChem: compound_name -> inchikey</option>
+        <option value="compound_name isomeric_smiles PubChem">PubChem: compound_name -> isomeric_smiles</option>
+        <option value="compound_name iupac_name PubChem">PubChem: compound_name -> iupac_name</option>
+        <option value="inchi canonical_smiles PubChem">PubChem: inchi -> canonical_smiles</option>
+        <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
+        <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
+        <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="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option>
+        <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option>
+        <option value="chebiid chemspiderid BridgeDB">BridgeDB: chebiid -> chemspiderid</option>
+        <option value="chebiid hmdbid BridgeDB">BridgeDB: chebiid -> hmdbid</option>
+        <option value="chebiid pubchemid BridgeDB">BridgeDB: chebiid -> pubchemid</option>
+        <option value="chebiid wikidataid BridgeDB">BridgeDB: chebiid -> wikidataid</option>
+        <option value="chemspiderid chebiid BridgeDB">BridgeDB: chemspiderid -> chebiid</option>
+        <option value="chemspiderid hmdbid BridgeDB">BridgeDB: chemspiderid -> hmdbid</option>
+        <option value="chemspiderid pubchemid BridgeDB">BridgeDB: chemspiderid -> pubchemid</option>
+        <option value="chemspiderid wikidataid BridgeDB">BridgeDB: chemspiderid -> wikidataid</option>
+        <option value="hmdbid chebiid BridgeDB">BridgeDB: hmdbid -> chebiid</option>
+        <option value="hmdbid chemspiderid BridgeDB">BridgeDB: hmdbid -> chemspiderid</option>
+        <option value="hmdbid pubchemid BridgeDB">BridgeDB: hmdbid -> pubchemid</option>
+        <option value="hmdbid wikidataid BridgeDB">BridgeDB: hmdbid -> wikidataid</option>
+        <option value="pubchemid chebiid BridgeDB">BridgeDB: pubchemid -> chebiid</option>
+        <option value="pubchemid chemspiderid BridgeDB">BridgeDB: pubchemid -> chemspiderid</option>
+        <option value="pubchemid hmdbid BridgeDB">BridgeDB: pubchemid -> hmdbid</option>
+        <option value="pubchemid wikidataid BridgeDB">BridgeDB: pubchemid -> wikidataid</option>
+        <option value="wikidataid chebiid BridgeDB">BridgeDB: wikidataid -> chebiid</option>
+        <option value="wikidataid chemspiderid BridgeDB">BridgeDB: wikidataid -> chemspiderid</option>
+        <option value="wikidataid hmdbid BridgeDB">BridgeDB: wikidataid -> hmdbid</option>
+        <option value="wikidataid pubchemid BridgeDB">BridgeDB: wikidataid -> pubchemid</option>
     </xml>
 
 </macros>
--- a/msmetaenhancer.xml	Tue Feb 15 12:26:04 2022 +0000
+++ b/msmetaenhancer.xml	Tue Mar 22 15:33:04 2022 +0000
@@ -66,6 +66,7 @@
     <tests>
         <test>
             <param name="input_file" value="sample.msp" ftype="msp" />
+            <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
             <output name="output_file" file="sample_out.msp" ftype="msp"/>
         </test>
     </tests>
--- a/msmetaenhancer_wrapper.py	Tue Feb 15 12:26:04 2022 +0000
+++ b/msmetaenhancer_wrapper.py	Tue Mar 22 15:33:04 2022 +0000
@@ -23,7 +23,7 @@
     app.curate_spectra()
 
     # specify requested services and jobs
-    services = ['PubChem', 'CTS', 'CIR', 'NLM']
+    services = ['PubChem', 'CTS', 'CIR', 'NLM', 'RDKit', 'IDSM', 'BridgeDB']
 
     if len(args.jobs) != 0:
         jobs = []
--- a/test-data/sample_out.msp	Tue Feb 15 12:26:04 2022 +0000
+++ b/test-data/sample_out.msp	Tue Mar 22 15:33:04 2022 +0000
@@ -1,43 +1,34 @@
-NAME: Hydrogen
 FORMULA: H2
 MW: 2
 CASNO: 1333-74-0
 ID: 1
 COMMENT: NIST MS# 245692, Seq# M1
-CANONICAL_SMILES: [HH]
+COMPOUND_NAME: Hydrogen
 INCHI: InChI=1S/H2/h1H
-INCHIKEY: UFHFLCQGNIYNRP-UHFFFAOYSA-N
-ISOMERIC_SMILES: [HH]
-IUPAC_NAME: molecular hydrogen
-SMILES: [H][H]
+CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
 1.0         20.98
 2.0         999.0
 
-NAME: Deuterium
 FORMULA: D2
 MW: 4
 CASNO: 7782-39-0
 ID: 2
 COMMENT: NIST MS# 61316, Seq# M2
-CANONICAL_SMILES: [HH]
+COMPOUND_NAME: Deuterium
 INCHI: InChI=1S/H2/h1H/i1+1D
-INCHIKEY: UFHFLCQGNIYNRP-VVKOMZTBSA-N
-ISOMERIC_SMILES: [2H][2H]
-SMILES: [2H][2H]
+CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
 2.0         14.99
 4.0         999.0
 
-NAME: Methane
 FORMULA: CH4
 MW: 16
 CASNO: 74-82-8
 ID: 3
 COMMENT: Any=100 ; NIST MS# 61313, Seq# M64
+COMPOUND_NAME: Methane
 INCHI: InChI=1S/CH4/h1H4
-INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-IUPAC_NAME: methane
 NUM PEAKS: 6
 12.0        37.97
 13.0        105.9
@@ -46,15 +37,13 @@
 16.0        999.0
 17.0        15.99
 
-NAME: Methane
 FORMULA: CH4
 MW: 16
 CASNO: 74-82-8
 ID: 4
 COMMENT: Any=100 ; NIST MS# 18807, Seq# R26
+COMPOUND_NAME: Methane
 INCHI: InChI=1S/CH4/h1H4
-INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-IUPAC_NAME: methane
 NUM PEAKS: 6
 12.0        25.98
 13.0        85.92
@@ -63,15 +52,13 @@
 16.0        999.0
 17.0        10.99
 
-NAME: Methane
 FORMULA: CH4
 MW: 16
 CASNO: 74-82-8
 ID: 5
 COMMENT: Any=100 ; NIST MS# 18809, Seq# R27
+COMPOUND_NAME: Methane
 INCHI: InChI=1S/CH4/h1H4
-INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-IUPAC_NAME: methane
 NUM PEAKS: 6
 12.0        7.99
 13.0        28.97
@@ -80,15 +67,13 @@
 16.0        999.0
 17.0        11.99
 
-NAME: Methane
 FORMULA: CH4
 MW: 16
 CASNO: 74-82-8
 ID: 6
 COMMENT: Any=100 ; NIST MS# 423924, Seq# R28
+COMPOUND_NAME: Methane
 INCHI: InChI=1S/CH4/h1H4
-INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-IUPAC_NAME: methane
 NUM PEAKS: 6
 12.0        25.98
 13.0        74.93