Mercurial > repos > recetox > msmetaenhancer

annotate macros.xml @ 11:791bf4d9b06c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
author recetox
date Tue, 16 Apr 2024 11:23:32 +0000
parents 3e2cb0bc6959
children a6af1e124e06
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ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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1 <macros>
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791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
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2 <token name="@TOOL_VERSION@">0.4.0</token>
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4 <xml name="creator">
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5 <creator>
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6 <person
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7 givenName="Matej"
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8 familyName="Troják"
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9 url="https://github.com/xtrojak"
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10 identifier="0000-0003-0841-2707" />
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11 <organization
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12 url="https://www.recetox.muni.cz/"
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13 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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14 name="RECETOX MUNI" />
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15 </creator>
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16 </xml>
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18 <token name="@HELP@">
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19 <![CDATA[
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2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
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20 MSMetaEnhancer will fetch and update various metadata included in your spectra dataset.
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21 It does so through a series of conversions ran on all entries in a given file. These conversions fetch
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22 metadata from various online services. If no conversions are specified, all possible jobs will be executed in an arbitrary order.
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24 Every conversion specifies `service`, `source` and `target` attributes. This can be read as the `service` will receive the `source` attribute
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25 and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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26 InChI to SMILES.
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28 The execution speed and results themselves can be affected by specifying the conversions, or their order.
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30 For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/.
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3e2cb0bc6959 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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32 ## Developer instructions
3e2cb0bc6959 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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3e2cb0bc6959 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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34 When updating this tool, it is necessary to make sure that `job_options` in `macros.xml` config file are up-to-date.
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35 This can be done by running `galaxy/generate_options.py` script in [MSMetaEnhancer](https://github.com/RECETOX/MSMetaEnhancer) tool and
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36 copying generated options to the macro.
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37
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38 ]]>
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39 </token>
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41 <xml name="job_options">
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42 <option value="canonical_smiles mw RDKit">RDKit: canonical_smiles -> mw</option>
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43 <option value="formula mw RDKit">RDKit: formula -> mw</option>
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44 <option value="inchi canonical_smiles RDKit">RDKit: inchi -> canonical_smiles</option>
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45 <option value="inchi isomeric_smiles RDKit">RDKit: inchi -> isomeric_smiles</option>
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46 <option value="isomeric_smiles mw RDKit">RDKit: isomeric_smiles -> mw</option>
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47 <option value="smiles mw RDKit">RDKit: smiles -> mw</option>
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48 <option value="compound_name canonical_smiles IDSM">IDSM: compound_name -> canonical_smiles</option>
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49 <option value="compound_name formula IDSM">IDSM: compound_name -> formula</option>
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50 <option value="compound_name inchi IDSM">IDSM: compound_name -> inchi</option>
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51 <option value="compound_name inchikey IDSM">IDSM: compound_name -> inchikey</option>
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52 <option value="compound_name isomeric_smiles IDSM">IDSM: compound_name -> isomeric_smiles</option>
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53 <option value="compound_name iupac_name IDSM">IDSM: compound_name -> iupac_name</option>
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54 <option value="inchi canonical_smiles IDSM">IDSM: inchi -> canonical_smiles</option>
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55 <option value="inchi formula IDSM">IDSM: inchi -> formula</option>
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56 <option value="inchi inchikey IDSM">IDSM: inchi -> inchikey</option>
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57 <option value="inchi isomeric_smiles IDSM">IDSM: inchi -> isomeric_smiles</option>
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58 <option value="inchi iupac_name IDSM">IDSM: inchi -> iupac_name</option>
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59 <option value="iupac_name inchi IDSM">IDSM: iupac_name -> inchi</option>
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60 <option value="casno inchi CTS">CTS: casno -> inchi</option>
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61 <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
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62 <option value="compound_name inchikey CTS">CTS: compound_name -> inchikey</option>
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63 <option value="hmdbid inchi CTS">CTS: hmdbid -> inchi</option>
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64 <option value="inchikey compound_name CTS">CTS: inchikey -> compound_name</option>
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65 <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
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66 <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
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67 <option value="casno smiles CIR">CIR: casno -> smiles</option>
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68 <option value="inchi smiles CIR">CIR: inchi -> smiles</option>
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69 <option value="inchikey casno CIR">CIR: inchikey -> casno</option>
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70 <option value="inchikey formula CIR">CIR: inchikey -> formula</option>
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71 <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option>
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72 <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option>
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73 <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option>
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74 <option value="compound_name canonical_smiles PubChem">PubChem: compound_name -> canonical_smiles</option>
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75 <option value="compound_name formula PubChem">PubChem: compound_name -> formula</option>
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76 <option value="compound_name inchi PubChem">PubChem: compound_name -> inchi</option>
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77 <option value="compound_name inchikey PubChem">PubChem: compound_name -> inchikey</option>
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78 <option value="compound_name isomeric_smiles PubChem">PubChem: compound_name -> isomeric_smiles</option>
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79 <option value="compound_name iupac_name PubChem">PubChem: compound_name -> iupac_name</option>
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80 <option value="inchi canonical_smiles PubChem">PubChem: inchi -> canonical_smiles</option>
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81 <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
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82 <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
83 <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
84 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
85 <option value="inchi pubchemid PubChem">PubChem: inchi -> pubchemid</option>
11
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
86 <option value="inchikey canonical_smiles PubChem">PubChem: inchikey -> canonical_smiles</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
87 <option value="inchikey formula PubChem">PubChem: inchikey -> formula</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
88 <option value="inchikey inchi PubChem">PubChem: inchikey -> inchi</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
89 <option value="inchikey isomeric_smiles PubChem">PubChem: inchikey -> isomeric_smiles</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
90 <option value="inchikey iupac_name PubChem">PubChem: inchikey -> iupac_name</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
91 <option value="inchikey pubchemid PubChem">PubChem: inchikey -> pubchemid</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
92 <option value="pubchemid canonical_smiles PubChem">PubChem: pubchemid -> canonical_smiles</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
93 <option value="pubchemid formula PubChem">PubChem: pubchemid -> formula</option>
0
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
94 <option value="pubchemid hmdbid PubChem">PubChem: pubchemid -> hmdbid</option>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
95 <option value="pubchemid inchi PubChem">PubChem: pubchemid -> inchi</option>
11
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
96 <option value="pubchemid inchikey PubChem">PubChem: pubchemid -> inchikey</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
97 <option value="pubchemid isomeric_smiles PubChem">PubChem: pubchemid -> isomeric_smiles</option>
791bf4d9b06c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 17a9f7a879086d08cd5e8ce11f2eb22f1e054ea5
recetox
parents: 10
diff changeset
98 <option value="pubchemid iupac_name PubChem">PubChem: pubchemid -> iupac_name</option>
8
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
99 <option value="chebiid chemspiderid BridgeDb">BridgeDb: chebiid -> chemspiderid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
100 <option value="chebiid hmdbid BridgeDb">BridgeDb: chebiid -> hmdbid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
101 <option value="chebiid keggid BridgeDb">BridgeDb: chebiid -> keggid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
102 <option value="chebiid pubchemid BridgeDb">BridgeDb: chebiid -> pubchemid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
103 <option value="chebiid wikidataid BridgeDb">BridgeDb: chebiid -> wikidataid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
104 <option value="chemspiderid chebiid BridgeDb">BridgeDb: chemspiderid -> chebiid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
105 <option value="chemspiderid hmdbid BridgeDb">BridgeDb: chemspiderid -> hmdbid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
106 <option value="chemspiderid keggid BridgeDb">BridgeDb: chemspiderid -> keggid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
107 <option value="chemspiderid pubchemid BridgeDb">BridgeDb: chemspiderid -> pubchemid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
108 <option value="chemspiderid wikidataid BridgeDb">BridgeDb: chemspiderid -> wikidataid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
109 <option value="hmdbid chebiid BridgeDb">BridgeDb: hmdbid -> chebiid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
110 <option value="hmdbid chemspiderid BridgeDb">BridgeDb: hmdbid -> chemspiderid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
111 <option value="hmdbid keggid BridgeDb">BridgeDb: hmdbid -> keggid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
112 <option value="hmdbid pubchemid BridgeDb">BridgeDb: hmdbid -> pubchemid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
113 <option value="hmdbid wikidataid BridgeDb">BridgeDb: hmdbid -> wikidataid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
114 <option value="keggid chebiid BridgeDb">BridgeDb: keggid -> chebiid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
115 <option value="keggid chemspiderid BridgeDb">BridgeDb: keggid -> chemspiderid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
116 <option value="keggid hmdbid BridgeDb">BridgeDb: keggid -> hmdbid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
117 <option value="keggid pubchemid BridgeDb">BridgeDb: keggid -> pubchemid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
118 <option value="keggid wikidataid BridgeDb">BridgeDb: keggid -> wikidataid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
119 <option value="pubchemid chebiid BridgeDb">BridgeDb: pubchemid -> chebiid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
120 <option value="pubchemid chemspiderid BridgeDb">BridgeDb: pubchemid -> chemspiderid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
121 <option value="pubchemid hmdbid BridgeDb">BridgeDb: pubchemid -> hmdbid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
122 <option value="pubchemid keggid BridgeDb">BridgeDb: pubchemid -> keggid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
123 <option value="pubchemid wikidataid BridgeDb">BridgeDb: pubchemid -> wikidataid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
124 <option value="wikidataid chebiid BridgeDb">BridgeDb: wikidataid -> chebiid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
125 <option value="wikidataid chemspiderid BridgeDb">BridgeDb: wikidataid -> chemspiderid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
126 <option value="wikidataid hmdbid BridgeDb">BridgeDb: wikidataid -> hmdbid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
127 <option value="wikidataid keggid BridgeDb">BridgeDb: wikidataid -> keggid</option>
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
recetox
parents: 6
diff changeset
128 <option value="wikidataid pubchemid BridgeDb">BridgeDb: wikidataid -> pubchemid</option>
0
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
129 </xml>
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
130
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
recetox
parents:
diff changeset
131 </macros>