Mercurial > repos > recetox > msmetaenhancer
comparison macros.xml @ 8:2ada1099f42e draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
| author | recetox |
|---|---|
| date | Thu, 18 May 2023 12:57:50 +0000 |
| parents | a2bf129850ea |
| children | 3e2cb0bc6959 |
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| 7:37afe368348b | 8:2ada1099f42e |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@TOOL_VERSION@">0.2.5</token> | 2 <token name="@TOOL_VERSION@">0.3.0</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" |
| 15 </creator> | 15 </creator> |
| 16 </xml> | 16 </xml> |
| 17 | 17 |
| 18 <token name="@HELP@"> | 18 <token name="@HELP@"> |
| 19 <![CDATA[ | 19 <![CDATA[ |
| 20 MSMetaEnhancer will fetch and update various metadata included in your spectra .msp dataset. | 20 MSMetaEnhancer will fetch and update various metadata included in your spectra dataset. |
| 21 It does so through a series of conversions ran on all entries in a given file. These conversions fetch | 21 It does so through a series of conversions ran on all entries in a given file. These conversions fetch |
| 22 metadata from various online services. If no conversions are specified, all possible jobs will be executed in an arbitrary order. | 22 metadata from various online services. If no conversions are specified, all possible jobs will be executed in an arbitrary order. |
| 23 | 23 |
| 24 Every conversion specifies `service`, `source` and `target` attributes. This can be read as the `service` will receive the `source` attribute | 24 Every conversion specifies `service`, `source` and `target` attributes. This can be read as the `service` will receive the `source` attribute |
| 25 and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert | 25 and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert |
| 31 ]]> | 31 ]]> |
| 32 </token> | 32 </token> |
| 33 | 33 |
| 34 <xml name="job_options"> | 34 <xml name="job_options"> |
| 35 <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option> | 35 <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option> |
| 36 <option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option> | |
| 37 <option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option> | |
| 36 <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option> | 38 <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option> |
| 37 <option value="smiles mw RDKit">RDKit: smiles -> mw</option> | 39 <option value="smiles mw RDKit">RDKit: smiles -> mw</option> |
| 38 <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option> | 40 <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option> |
| 39 <option value="compound_name formula IDSM">IDSM: compound_name -> formula</option> | 41 <option value="compound_name formula IDSM">IDSM: compound_name -> formula</option> |
| 40 <option value="compound_name inchi IDSM">IDSM: compound_name -> inchi</option> | 42 <option value="compound_name inchi IDSM">IDSM: compound_name -> inchi</option> |
| 59 <option value="inchikey casno CIR">CIR: inchikey -> casno</option> | 61 <option value="inchikey casno CIR">CIR: inchikey -> casno</option> |
| 60 <option value="inchikey formula CIR">CIR: inchikey -> formula</option> | 62 <option value="inchikey formula CIR">CIR: inchikey -> formula</option> |
| 61 <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option> | 63 <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option> |
| 62 <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option> | 64 <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option> |
| 63 <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option> | 65 <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option> |
| 64 <option value="compound_name casno NLM">NLM: compound_name -> casno</option> | |
| 65 <option value="compound_name formula NLM">NLM: compound_name -> formula</option> | |
| 66 <option value="compound_name inchikey NLM">NLM: compound_name -> inchikey</option> | |
| 67 <option value="inchikey casno NLM">NLM: inchikey -> casno</option> | |
| 68 <option value="inchikey compound_name NLM">NLM: inchikey -> compound_name</option> | |
| 69 <option value="inchikey formula NLM">NLM: inchikey -> formula</option> | |
| 70 <option value="compound_name canonical_smiles PubChem">PubChem: compound_name -> canonical_smiles</option> | 66 <option value="compound_name canonical_smiles PubChem">PubChem: compound_name -> canonical_smiles</option> |
| 71 <option value="compound_name formula PubChem">PubChem: compound_name -> formula</option> | 67 <option value="compound_name formula PubChem">PubChem: compound_name -> formula</option> |
| 72 <option value="compound_name inchi PubChem">PubChem: compound_name -> inchi</option> | 68 <option value="compound_name inchi PubChem">PubChem: compound_name -> inchi</option> |
| 73 <option value="compound_name inchikey PubChem">PubChem: compound_name -> inchikey</option> | 69 <option value="compound_name inchikey PubChem">PubChem: compound_name -> inchikey</option> |
| 74 <option value="compound_name isomeric_smiles PubChem">PubChem: compound_name -> isomeric_smiles</option> | 70 <option value="compound_name isomeric_smiles PubChem">PubChem: compound_name -> isomeric_smiles</option> |
| 79 <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option> | 75 <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option> |
| 80 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option> | 76 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option> |
| 81 <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option> | 77 <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option> |
| 82 <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option> | 78 <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option> |
| 83 <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option> | 79 <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option> |
| 84 <option value="chebiid chemspiderid BridgeDB">BridgeDB: chebiid -> chemspiderid</option> | 80 <option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option> |
| 85 <option value="chebiid hmdbid BridgeDB">BridgeDB: chebiid -> hmdbid</option> | 81 <option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option> |
| 86 <option value="chebiid keggid BridgeDB">BridgeDB: chebiid -> keggid</option> | 82 <option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option> |
| 87 <option value="chebiid pubchemid BridgeDB">BridgeDB: chebiid -> pubchemid</option> | 83 <option value="chebiid pubchemid BridgeDb">BridgeDb: chebiid -> pubchemid</option> |
| 88 <option value="chebiid wikidataid BridgeDB">BridgeDB: chebiid -> wikidataid</option> | 84 <option value="chebiid wikidataid BridgeDb">BridgeDb: chebiid -> wikidataid</option> |
| 89 <option value="chemspiderid chebiid BridgeDB">BridgeDB: chemspiderid -> chebiid</option> | 85 <option value="chemspiderid chebiid BridgeDb">BridgeDb: chemspiderid -> chebiid</option> |
| 90 <option value="chemspiderid hmdbid BridgeDB">BridgeDB: chemspiderid -> hmdbid</option> | 86 <option value="chemspiderid hmdbid BridgeDb">BridgeDb: chemspiderid -> hmdbid</option> |
| 91 <option value="chemspiderid keggid BridgeDB">BridgeDB: chemspiderid -> keggid</option> | 87 <option value="chemspiderid keggid BridgeDb">BridgeDb: chemspiderid -> keggid</option> |
| 92 <option value="chemspiderid pubchemid BridgeDB">BridgeDB: chemspiderid -> pubchemid</option> | 88 <option value="chemspiderid pubchemid BridgeDb">BridgeDb: chemspiderid -> pubchemid</option> |
| 93 <option value="chemspiderid wikidataid BridgeDB">BridgeDB: chemspiderid -> wikidataid</option> | 89 <option value="chemspiderid wikidataid BridgeDb">BridgeDb: chemspiderid -> wikidataid</option> |
| 94 <option value="hmdbid chebiid BridgeDB">BridgeDB: hmdbid -> chebiid</option> | 90 <option value="hmdbid chebiid BridgeDb">BridgeDb: hmdbid -> chebiid</option> |
| 95 <option value="hmdbid chemspiderid BridgeDB">BridgeDB: hmdbid -> chemspiderid</option> | 91 <option value="hmdbid chemspiderid BridgeDb">BridgeDb: hmdbid -> chemspiderid</option> |
| 96 <option value="hmdbid keggid BridgeDB">BridgeDB: hmdbid -> keggid</option> | 92 <option value="hmdbid keggid BridgeDb">BridgeDb: hmdbid -> keggid</option> |
| 97 <option value="hmdbid pubchemid BridgeDB">BridgeDB: hmdbid -> pubchemid</option> | 93 <option value="hmdbid pubchemid BridgeDb">BridgeDb: hmdbid -> pubchemid</option> |
| 98 <option value="hmdbid wikidataid BridgeDB">BridgeDB: hmdbid -> wikidataid</option> | 94 <option value="hmdbid wikidataid BridgeDb">BridgeDb: hmdbid -> wikidataid</option> |
| 99 <option value="keggid chebiid BridgeDB">BridgeDB: keggid -> chebiid</option> | 95 <option value="keggid chebiid BridgeDb">BridgeDb: keggid -> chebiid</option> |
| 100 <option value="keggid chemspiderid BridgeDB">BridgeDB: keggid -> chemspiderid</option> | 96 <option value="keggid chemspiderid BridgeDb">BridgeDb: keggid -> chemspiderid</option> |
| 101 <option value="keggid hmdbid BridgeDB">BridgeDB: keggid -> hmdbid</option> | 97 <option value="keggid hmdbid BridgeDb">BridgeDb: keggid -> hmdbid</option> |
| 102 <option value="keggid pubchemid BridgeDB">BridgeDB: keggid -> pubchemid</option> | 98 <option value="keggid pubchemid BridgeDb">BridgeDb: keggid -> pubchemid</option> |
| 103 <option value="keggid wikidataid BridgeDB">BridgeDB: keggid -> wikidataid</option> | 99 <option value="keggid wikidataid BridgeDb">BridgeDb: keggid -> wikidataid</option> |
| 104 <option value="pubchemid chebiid BridgeDB">BridgeDB: pubchemid -> chebiid</option> | 100 <option value="pubchemid chebiid BridgeDb">BridgeDb: pubchemid -> chebiid</option> |
| 105 <option value="pubchemid chemspiderid BridgeDB">BridgeDB: pubchemid -> chemspiderid</option> | 101 <option value="pubchemid chemspiderid BridgeDb">BridgeDb: pubchemid -> chemspiderid</option> |
| 106 <option value="pubchemid hmdbid BridgeDB">BridgeDB: pubchemid -> hmdbid</option> | 102 <option value="pubchemid hmdbid BridgeDb">BridgeDb: pubchemid -> hmdbid</option> |
| 107 <option value="pubchemid keggid BridgeDB">BridgeDB: pubchemid -> keggid</option> | 103 <option value="pubchemid keggid BridgeDb">BridgeDb: pubchemid -> keggid</option> |
| 108 <option value="pubchemid wikidataid BridgeDB">BridgeDB: pubchemid -> wikidataid</option> | 104 <option value="pubchemid wikidataid BridgeDb">BridgeDb: pubchemid -> wikidataid</option> |
| 109 <option value="wikidataid chebiid BridgeDB">BridgeDB: wikidataid -> chebiid</option> | 105 <option value="wikidataid chebiid BridgeDb">BridgeDb: wikidataid -> chebiid</option> |
| 110 <option value="wikidataid chemspiderid BridgeDB">BridgeDB: wikidataid -> chemspiderid</option> | 106 <option value="wikidataid chemspiderid BridgeDb">BridgeDb: wikidataid -> chemspiderid</option> |
| 111 <option value="wikidataid hmdbid BridgeDB">BridgeDB: wikidataid -> hmdbid</option> | 107 <option value="wikidataid hmdbid BridgeDb">BridgeDb: wikidataid -> hmdbid</option> |
| 112 <option value="wikidataid keggid BridgeDB">BridgeDB: wikidataid -> keggid</option> | 108 <option value="wikidataid keggid BridgeDb">BridgeDb: wikidataid -> keggid</option> |
| 113 <option value="wikidataid pubchemid BridgeDB">BridgeDB: wikidataid -> pubchemid</option> | 109 <option value="wikidataid pubchemid BridgeDb">BridgeDb: wikidataid -> pubchemid</option> |
| 114 </xml> | 110 </xml> |
| 115 | 111 |
| 116 </macros> | 112 </macros> |