Mercurial > repos > recetox > msmetaenhancer

annotate macros.xml @ 1:4c328e0e59ab draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:23:58 +0000
parents 053ce79ed564
children 4ae5b466a805
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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1 <macros>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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2 <token name="@TOOL_VERSION@">0.1.2</token>
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4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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4 <xml name="creator">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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5 <creator>
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4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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6 <person
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 givenName="Matej"
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 familyName="Troják"
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 url="https://github.com/xtrojak"
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 identifier="0000-0003-0841-2707" />
0
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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11 <organization
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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12 url="https://www.recetox.muni.cz/"
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4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
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053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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14 name="RECETOX MUNI" />
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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15 </creator>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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16 </xml>
1
4c328e0e59ab "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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0
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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18 <token name="@HELP@">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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19 <![CDATA[
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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20 MSMetaEnhancer will fetch and update various metadata included in your spectra .msp dataset.
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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21 It does so through a series of conversions ran on all entries in a given file. These conversions fetch
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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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.
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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23
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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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
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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25 and based on that determines the `target` attribute. For example, the conversion `PubChem: inchi -> smiles` uses PubChem to convert
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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26 InChI to SMILES.
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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27
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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28 The execution speed and results themselves can be affected by specifying the conversions, or their order.
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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29
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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30 For detailed documentation of the tool please visit https://msmetaenhancer.readthedocs.io/.
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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31 ]]>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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32 </token>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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33
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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34 <xml name="job_options">
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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35 <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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36 <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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37 <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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38 <option value="inchi smiles PubChem">PubChem: inchi -> smiles</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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39 <option value="name formula PubChem">PubChem: name -> formula</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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40 <option value="name inchi PubChem">PubChem: name -> inchi</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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41 <option value="name inchikey PubChem">PubChem: name -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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42 <option value="name iupac_name PubChem">PubChem: name -> iupac_name</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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43 <option value="name smiles PubChem">PubChem: name -> smiles</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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44 <option value="casno smiles CIR">CIR: casno -> smiles</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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45 <option value="inchikey casno CIR">CIR: inchikey -> casno</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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46 <option value="inchikey formula CIR">CIR: inchikey -> formula</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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47 <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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48 <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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49 <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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50 <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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51 <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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52 <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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53 <option value="inchikey name CTS">CTS: inchikey -> name</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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54 <option value="name inchikey CTS">CTS: name -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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55 <option value="inchikey casno NLM">NLM: inchikey -> casno</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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56 <option value="inchikey formula NLM">NLM: inchikey -> formula</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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57 <option value="inchikey name NLM">NLM: inchikey -> name</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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58 <option value="name casno NLM">NLM: name -> casno</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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59 <option value="name formula NLM">NLM: name -> formula</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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60 <option value="name inchikey NLM">NLM: name -> inchikey</option>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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61 </xml>
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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62
053ce79ed564 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 2c9c75f7d0c5fcadf1fe0284dd767ea5c6f6be51"
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63 </macros>