Mercurial > repos > recetox > recetox_xmsannotator_simple

annotate macros.xml @ 3:b8b1b865c82d draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
author recetox
date Thu, 12 Aug 2021 11:27:50 +0000
parents c72233720bdc
children 6d9cda26796e
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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1 <macros>
c72233720bdc "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>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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3 <xml name="requirements">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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4 <requirements>
c72233720bdc "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>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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6 </requirements>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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7 </xml>
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b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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8 <xml name="creator">
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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9 <creator>
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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10 <organization
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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11 url="https://www.recetox.muni.cz/"
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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12 name="RECETOX MUNI" />
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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13 </creator>
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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14 </xml>
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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15 <xml name="inputs">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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16 <param name="peak_table" type="data" format="csv,h5,parquet">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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17 <label>Peak table</label>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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18 <help><![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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19 A peak-intensity table such as outputted from apLCMS.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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20 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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21 ]]></help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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22 </param>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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23 <param name="compound_table" type="data" format="csv,parquet">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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24 <label>Compound database</label>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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25 <help><![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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26 Database of compounds according to which the annotation is performed.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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27 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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28 ]]></help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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29 </param>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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30 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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31 <label>Adduct database (optional)</label>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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32 <help><![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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33 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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34 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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35 ]]></help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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36 </param>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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37 </xml>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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39 <xml name="outputs">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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40 <data name="annotation_parquet" format="parquet"/>
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41 </xml>
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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43 <xml name="tolerance">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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44 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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45 <label>Mass tolerance [ppm]</label>
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46 <help>Mass tolerance in ppm for database matching.</help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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47 </param>
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48 <yield/>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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49 </xml>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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50 <token name="@HELP@">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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51 <![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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52 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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53 using advanced methods.
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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54
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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55 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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56 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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57 withing some tolerance.
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58 ]]>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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59 </token>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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60 <xml name="citations">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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61 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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62 </xml>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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63 </macros>