Mercurial > repos > recetox > recetox_xmsannotator_advanced
annotate macros.xml @ 1:2c6fa447f6a0 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 8547c5323747595eabbeed29039a1b2363491243
author | recetox |
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date | Thu, 20 Jul 2023 06:29:06 +0000 |
parents | cfd2e19f00a9 |
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cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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1 <macros> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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2 <token name="@TOOL_VERSION@">0.10.0</token> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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3 |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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4 <xml name="requirements"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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5 <requirements> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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6 <requirement type="package" version="@TOOL_VERSION@">r-recetox-xmsannotator</requirement> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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7 </requirements> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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8 </xml> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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9 |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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10 <xml name="creator"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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11 <creator> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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12 <person |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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13 givenName="Jiří" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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14 familyName="Novotný" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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15 url="https://github.com/xtracko" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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16 identifier="0000-0001-5449-3523" /> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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17 <person |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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18 givenName="Martin" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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19 familyName="Čech" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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20 url="https://github.com/martenson" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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21 identifier="0000-0002-9318-1781" /> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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22 <person |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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23 givenName="Matej" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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24 familyName="Troják" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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25 url="https://github.com/xtrojak" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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26 identifier="0000-0003-0841-2707" /> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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27 <organization |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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28 url="https://www.recetox.muni.cz/" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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30 name="RECETOX MUNI" /> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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31 </creator> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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32 </xml> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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33 |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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34 <xml name="inputs"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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35 <param name="metadata_table" type="data" format="parquet,csv"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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36 <label>Metadata table</label> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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37 <help><![CDATA[ |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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38 Peak metadata table*. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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39 ]]></help> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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40 </param> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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41 <param name="intensity_table" type="data" format="parquet,csv"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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42 <label>Intensity table</label> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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43 <help><![CDATA[ |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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44 Table with intensities** for features (rows) across samples (columns). |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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45 ]]></help> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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46 </param> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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47 <param name="compound_table" type="data" format="parquet,csv"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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48 <label>Compound database</label> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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49 <help><![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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50 Database of compounds according to which the annotation is performed. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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51 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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52 ]]></help> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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53 </param> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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54 <param name="adduct_table" type="data" format="parquet,csv" optional="true"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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55 <label>Adduct database</label> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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56 <help><![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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57 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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58 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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59 ]]></help> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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60 </param> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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61 <param name="adduct_weights" type="data" format="parquet,csv" optional="true"> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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62 <label>Adduct weights</label> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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63 <help> |
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64 A weight-by-adduct table. |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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65 </help> |
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66 </param> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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67 </xml> |
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68 |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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69 <xml name="outputs"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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70 <data name="output_file" format="parquet"> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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71 <change_format> |
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72 <when input="metadata_table.ext" value="csv" format="csv" /> |
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73 </change_format> |
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74 </data> |
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75 </xml> |
cfd2e19f00a9
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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76 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
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77 <xml name="tolerance"> |
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78 <param name="mass_tolerance_ppm" type="integer" min="0" value="5"> |
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79 <label>Mass tolerance [ppm]</label> |
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80 <help>Mass tolerance in ppm for database matching.</help> |
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81 </param> |
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82 <yield/> |
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83 </xml> |
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84 |
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85 <token name="@HELP@"> |
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86 Description |
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87 =========== |
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88 |
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89 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database |
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90 using advanced methods. |
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91 |
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92 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured |
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93 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are |
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94 withing some tolerance. |
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95 |
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96 Then, a score and a confidence level is assigned to each match based on peak correlation |
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97 clustering, metabolite pathway associations, adducts expectations, and isotope conformations. |
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98 |
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99 Input tables description |
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100 ------------------------ |
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101 |
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102 (*) Metadata table |
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103 ~~~~~~~~~~~~~~~~~~ |
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104 |
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105 The output from recetox-aplcms tool. |
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106 The `npeaks` column denotes the number of peaks which have been grouped into this feature. |
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107 The columns with the sample names indicate whether this feature is present in the sample. |
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108 Only id, mz, and rt columns are required to be present. |
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109 |
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110 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ |
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111 | id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | |
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112 +=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+ |
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113 | 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 | |
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114 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ |
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115 | 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 | |
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116 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ |
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117 | 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 | |
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118 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ |
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119 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | |
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120 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+ |
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121 |
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122 (**) Intensity table |
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123 ~~~~~~~~~~~~~~~~~~~~ |
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124 |
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125 The output from recetox-aplcms tool. |
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126 This table contains the peak area for aligned features in all samples. |
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127 |
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128 +-------+------------------------+------------------------+------------------------+ |
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129 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq | |
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130 +=======+========================+========================+========================+ |
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131 | 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 | |
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132 +-------+------------------------+------------------------+------------------------+ |
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133 | 2 | 2075168.6398983458 | 0 | 2574362.159289044 | |
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134 +-------+------------------------+------------------------+------------------------+ |
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135 | 57 | 2934524.4406785755 | 1333044.5065971944 | 0 | |
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136 +-------+------------------------+------------------------+------------------------+ |
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137 | ... | ... | ... | ... | |
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138 +-------+------------------------+------------------------+------------------------+ |
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139 </token> |
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140 |
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141 <xml name="citations"> |
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142 <citation type="doi">10.1021/acs.analchem.6b01214</citation> |
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143 </xml> |
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144 </macros> |