Mercurial > repos > recetox > msmetaenhancer

diff macros.xml @ 11:25319f346ad4 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
author recetox
date Thu, 18 May 2023 12:57:39 +0000
parents 741b12b386d5
children f4a90c68e2de
line wrap: on
line diff
--- a/macros.xml	Tue May 09 09:18:00 2023 +0000
+++ b/macros.xml	Thu May 18 12:57:39 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.2.5</token>
+    <token name="@TOOL_VERSION@">0.3.0</token>
 
     <xml name="creator">
         <creator>
@@ -17,7 +17,7 @@
 
     <token name="@HELP@">
         <![CDATA[
-        MSMetaEnhancer will fetch and update various metadata included in your spectra .msp dataset.
+        MSMetaEnhancer will fetch and update various metadata included in your spectra dataset.
         It does so through a series of conversions ran on all entries in a given file. These conversions fetch
         metadata from various online services. If no conversions are specified, all possible jobs will be executed in an arbitrary order.
 
@@ -33,6 +33,8 @@
 
     <xml name="job_options">
         <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> 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>
         <option value="smiles mw RDKit">RDKit: smiles -> mw</option>
         <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option>
@@ -61,12 +63,6 @@
         <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="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>
@@ -81,36 +77,36 @@
         <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 keggid BridgeDB">BridgeDB: chebiid -> keggid</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 keggid BridgeDB">BridgeDB: chemspiderid -> keggid</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 keggid BridgeDB">BridgeDB: hmdbid -> keggid</option>
-        <option value="hmdbid pubchemid BridgeDB">BridgeDB: hmdbid -> pubchemid</option>
-        <option value="hmdbid wikidataid BridgeDB">BridgeDB: hmdbid -> wikidataid</option>
-        <option value="keggid chebiid BridgeDB">BridgeDB: keggid -> chebiid</option>
-        <option value="keggid chemspiderid BridgeDB">BridgeDB: keggid -> chemspiderid</option>
-        <option value="keggid hmdbid BridgeDB">BridgeDB: keggid -> hmdbid</option>
-        <option value="keggid pubchemid BridgeDB">BridgeDB: keggid -> pubchemid</option>
-        <option value="keggid wikidataid BridgeDB">BridgeDB: keggid -> 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 keggid BridgeDB">BridgeDB: pubchemid -> keggid</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 keggid BridgeDB">BridgeDB: wikidataid -> keggid</option>
-        <option value="wikidataid pubchemid BridgeDB">BridgeDB: wikidataid -> pubchemid</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>
+        <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 keggid BridgeDb">BridgeDb: chemspiderid -> keggid</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 keggid BridgeDb">BridgeDb: hmdbid -> keggid</option>
+        <option value="hmdbid pubchemid BridgeDb">BridgeDb: hmdbid -> pubchemid</option>
+        <option value="hmdbid wikidataid BridgeDb">BridgeDb: hmdbid -> wikidataid</option>
+        <option value="keggid chebiid BridgeDb">BridgeDb: keggid -> chebiid</option>
+        <option value="keggid chemspiderid BridgeDb">BridgeDb: keggid -> chemspiderid</option>
+        <option value="keggid hmdbid BridgeDb">BridgeDb: keggid -> hmdbid</option>
+        <option value="keggid pubchemid BridgeDb">BridgeDb: keggid -> pubchemid</option>
+        <option value="keggid wikidataid BridgeDb">BridgeDb: keggid -> 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 keggid BridgeDb">BridgeDb: pubchemid -> keggid</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 keggid BridgeDb">BridgeDb: wikidataid -> keggid</option>
+        <option value="wikidataid pubchemid BridgeDb">BridgeDb: wikidataid -> pubchemid</option>
     </xml>
 
 </macros>