diff macros.xml @ 0:ce612a11b455 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 22 15:33:37 2022 +0000
@@ -0,0 +1,106 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.2.0</token>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Matej"
+                familyName="Troják"
+                url="https://github.com/xtrojak"
+                identifier="0000-0003-0841-2707" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="[e-mail]"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+    <token name="@HELP@">
+        <![CDATA[
+        MSMetaEnhancer will fetch and update various metadata included in your spectra .msp 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.
+
+        Every conversion specifies `service`, `source` and `target` attributes. This can be read as the `service` will receive the `source` attribute
+        and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert
+        InChI to SMILES.
+
+        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/.
+    ]]>
+    </token>
+
+    <xml name="job_options">
+        <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="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>
+        <option value="inchikey formula CIR">CIR: inchikey -> formula</option>
+        <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>
+        <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>