Mercurial > repos > recetox > recetox_xmsannotator_advanced

annotate macros.xml @ 4:464c1e80a01f draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:27:30 +0000
parents 94209fea0a99
children a393c4383436
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7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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1 <macros>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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2 <token name="@TOOL_VERSION@">0.9.0</token>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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3 <xml name="requirements">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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4 <requirements>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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5 <requirement type="package" version="0.9.0">r-recetox-xmsannotator</requirement>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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6 </requirements>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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7 </xml>
3
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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8 <xml name="creator">
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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9 <creator>
4
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 <person
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11 givenName="Jiří"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 familyName="Novotný"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 url="https://github.com/xtracko"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 identifier="0000-0001-5449-3523" />
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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15 <person
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 givenName="Martin"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 familyName="Čech"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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18 url="https://github.com/martenson"
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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19 identifier="0000-0002-9318-1781" />
3
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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20 <organization
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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21 url="https://www.recetox.muni.cz/"
4
464c1e80a01f "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
3
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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23 name="RECETOX MUNI" />
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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24 </creator>
94209fea0a99 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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25 </xml>
2
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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26 <xml name="inputs">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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27 <param name="peak_table" type="data" format="csv,h5,parquet">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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28 <label>Peak table</label>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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29 <help><![CDATA[
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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30 A peak-intensity table such as outputted from apLCMS.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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31 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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32 ]]></help>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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33 </param>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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34 <param name="compound_table" type="data" format="csv,parquet">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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35 <label>Compound database</label>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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36 <help><![CDATA[
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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37 Database of compounds according to which the annotation is performed.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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38 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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39 ]]></help>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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40 </param>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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41 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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42 <label>Adduct database (optional)</label>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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43 <help><![CDATA[
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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44 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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45 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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46 ]]></help>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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47 </param>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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48 </xml>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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49
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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50 <xml name="outputs">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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51 <data name="annotation_parquet" format="parquet"/>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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52 </xml>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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53
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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54 <xml name="tolerance">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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55 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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56 <label>Mass tolerance [ppm]</label>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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57 <help>Mass tolerance in ppm for database matching.</help>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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58 </param>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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59 <yield/>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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60 </xml>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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61 <token name="@HELP@">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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62 <![CDATA[
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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63 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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64 using advanced methods.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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65
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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66 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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67 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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68 withing some tolerance.
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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69 ]]>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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70 </token>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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71 <xml name="citations">
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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72 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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73 </xml>
7807fbeb1388 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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74 </macros>