Mercurial > repos > recetox > xmsannotator_advanced

annotate xmsannotator_macros.xml @ 5:47185b5abe9e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
author recetox
date Mon, 14 Dec 2020 03:33:44 +0000
parents 3bdef6d114fd
children 53246490912c
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60aec5c0e1ea "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.2</token>
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3 <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox2</token>
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5 <xml name="inputs">
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6 <param name="peak_table" type="data" format="csv,h5,parquet">
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7 <label>Peak table</label>
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8 <help><![CDATA[
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9 A peak-intensity table such as outputted from apLCMS.
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10 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
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11 ]]></help>
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12 </param>
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13 <param name="compound_table" type="data" format="csv,parquet">
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14 <label>Compound database</label>
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15 <help><![CDATA[
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16 Database of compounds according to which the annotation is performed.
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17 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
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18 ]]></help>
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19 </param>
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20 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
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21 <label>Adduct database (optional)</label>
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22 <help><![CDATA[
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23 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
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24 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
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25 ]]></help>
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26 </param>
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27 </xml>
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29 <xml name="outputs">
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30 <data name="annotation_parquet" format="parquet"/>
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31 </xml>
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33 <xml name="tolerance">
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34 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
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35 <label>Mass tolerance [ppm]</label>
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36 <help>Mass tolerance in ppm for database matching.</help>
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37 </param>
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38 <yield/>
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39 </xml>
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41 <xml name="citations">
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42 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
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43 </xml>
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44 </macros>