Mercurial > repos > recetox > msmetaenhancer

diff macros.xml @ 13:f4a90c68e2de draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 1d1ecf792f5ea1c8a8f443dd1c3f55c810c5b00d
author recetox
date Mon, 27 May 2024 12:40:12 +0000
parents 25319f346ad4
children
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--- a/macros.xml	Thu Jun 22 14:10:33 2023 +0000
+++ b/macros.xml	Mon May 27 12:40:12 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>
@@ -28,11 +28,19 @@
         The execution speed and results themselves can be affected by specifying the conversions, or their order.
 
         For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/.
+
+        ## Developer instructions
+
+        When updating this tool, it is necessary to make sure that `job_options` in `macros.xml` config file are up-to-date.
+        This can be done by running `galaxy/generate_options.py` script in [MSMetaEnhancer](https://github.com/RECETOX/MSMetaEnhancer) tool and 
+        copying generated options to the macro.
+
     ]]>
     </token>
 
     <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>
@@ -75,8 +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>