Mercurial > repos > recetox > msmetaenhancer

comparison 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
comparison
equal deleted inserted replaced
12:5de89437323f 13:f4a90c68e2de
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.3.0</token> 2 <token name="@TOOL_VERSION@">0.4.0</token>
3 3
4 <xml name="creator"> 4 <xml name="creator">
5 <creator> 5 <creator>
6 <person 6 <person
7 givenName="Matej" 7 givenName="Matej"
26 InChI to SMILES. 26 InChI to SMILES.
27 27
28 The execution speed and results themselves can be affected by specifying the conversions, or their order. 28 The execution speed and results themselves can be affected by specifying the conversions, or their order.
29 29
30 For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/. 30 For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/.
31
32 ## Developer instructions
33
34 When updating this tool, it is necessary to make sure that `job_options` in `macros.xml` config file are up-to-date.
35 This can be done by running `galaxy/generate_options.py` script in [MSMetaEnhancer](https://github.com/RECETOX/MSMetaEnhancer) tool and
36 copying generated options to the macro.
37
31 ]]> 38 ]]>
32 </token> 39 </token>
33 40
34 <xml name="job_options"> 41 <xml name="job_options">
35 <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option> 42 <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option>
43 <option value="formula mw RDKit">RDKit: formula -> mw</option>
36 <option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option> 44 <option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option>
37 <option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option> 45 <option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option>
38 <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option> 46 <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option>
39 <option value="smiles mw RDKit">RDKit: smiles -> mw</option> 47 <option value="smiles mw RDKit">RDKit: smiles -> mw</option>
40 <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option> 48 <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option>
73 <option value="inchi formula PubChem">PubChem: inchi -> formula</option> 81 <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
74 <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option> 82 <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
75 <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option> 83 <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
76 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option> 84 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
77 <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option> 85 <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option>
86 <option value="inchikey canonical_smiles PubChem">PubChem: inchikey -> canonical_smiles</option>
87 <option value="inchikey formula PubChem">PubChem: inchikey -> formula</option>
88 <option value="inchikey inchi PubChem">PubChem: inchikey -> inchi</option>
89 <option value="inchikey isomeric_smiles PubChem">PubChem: inchikey -> isomeric_smiles</option>
90 <option value="inchikey iupac_name PubChem">PubChem: inchikey -> iupac_name</option>
91 <option value="inchikey pubchemid PubChem">PubChem: inchikey -> pubchemid</option>
92 <option value="pubchemid canonical_smiles PubChem">PubChem: pubchemid -> canonical_smiles</option>
93 <option value="pubchemid formula PubChem">PubChem: pubchemid -> formula</option>
78 <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option> 94 <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option>
79 <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option> 95 <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option>
96 <option value="pubchemid inchikey PubChem">PubChem: pubchemid -> inchikey</option>
97 <option value="pubchemid isomeric_smiles PubChem">PubChem: pubchemid -> isomeric_smiles</option>
98 <option value="pubchemid iupac_name PubChem">PubChem: pubchemid -> iupac_name</option>
80 <option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option> 99 <option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option>
81 <option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option> 100 <option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option>
82 <option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option> 101 <option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option>
83 <option value="chebiid pubchemid BridgeDb">BridgeDb: chebiid -> pubchemid</option> 102 <option value="chebiid pubchemid BridgeDb">BridgeDb: chebiid -> pubchemid</option>
84 <option value="chebiid wikidataid BridgeDb">BridgeDb: chebiid -> wikidataid</option> 103 <option value="chebiid wikidataid BridgeDb">BridgeDb: chebiid -> wikidataid</option>