Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

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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 16:24:26 +0000
parents a48e50d1dba3
children
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e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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1 <macros>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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2 <token name="@TOOL_VERSION@">0.9.0</token>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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3 <xml name="requirements">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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4 <requirements>
10
a48e50d1dba3 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b4b43f4f1e0633213a65aa57706bd997ac18f96b"
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5 <container type="docker">recetox/recetox-xmsannotator:october-conda0</container>
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e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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6 </requirements>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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7 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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8 <xml name="creator">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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9 <creator>
17
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 <person
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11 givenName="Martin"
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 familyName="Čech"
24034fff44e0 "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/martenson"
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 identifier="0000-0002-9318-1781" />
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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15 <organization
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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16 url="https://www.recetox.muni.cz/"
17
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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18 name="RECETOX MUNI" />
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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19 </creator>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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20 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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21 <xml name="inputs">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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22 <param name="peak_table" type="data" format="csv,parquet">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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23 <label>Peak table</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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24 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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25 A peak-intensity table such as outputted from apLCMS.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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26 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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27 Columns for feature intensity in a sample have to start with <em>intensity</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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28
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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29 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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30 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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31 <param name="compound_table" type="data" format="csv,parquet">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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32 <label>Compound database</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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33 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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34 Database of compounds according to which the annotation is performed.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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35 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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36 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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37 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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38 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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39 <label>Adduct database (optional)</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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40 <help><![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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41 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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42 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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43 ]]></help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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44 </param>
1
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
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45 <param name="adduct_weights" type="data" format="csv" optional="true">
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
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46 <label>adduct_weights</label>
8fcf5ca25f5d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
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47 </param>
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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48 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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49
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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50 <xml name="outputs">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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51 <data name="annotation_parquet" format="parquet"/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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52 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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53
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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54 <xml name="tolerance">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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55 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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56 <label>Mass tolerance [ppm]</label>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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57 <help>Mass tolerance in ppm for database matching.</help>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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58 </param>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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59 <yield/>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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60 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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61 <token name="@HELP@">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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62 <![CDATA[
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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63 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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64 using advanced methods.
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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65
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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66 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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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
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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68 withing some tolerance.
17
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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69
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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70 Then, a score and a confidence level is assigned to each match based on peak correlation
24034fff44e0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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71 clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
0
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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72 ]]>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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73 </token>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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74 <xml name="citations">
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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75 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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76 </xml>
e2e2e455fcfb "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
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77 </macros>