Mercurial > repos > recetox > recetox_xmsannotator_simple
comparison macros.xml @ 2:c72233720bdc draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
| author | recetox |
|---|---|
| date | Thu, 12 Aug 2021 11:12:32 +0000 |
| parents | |
| children | b8b1b865c82d |
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| 1:fa85bd6fd713 | 2:c72233720bdc |
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| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">0.9.0</token> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="0.9.0">r-recetox-xmsannotator</requirement> | |
| 6 </requirements> | |
| 7 </xml> | |
| 8 | |
| 9 <xml name="inputs"> | |
| 10 <param name="peak_table" type="data" format="csv,h5,parquet"> | |
| 11 <label>Peak table</label> | |
| 12 <help><![CDATA[ | |
| 13 A peak-intensity table such as outputted from apLCMS. | |
| 14 The file is required to contain the fields <em>mz</em> and <em>rt</em>. | |
| 15 ]]></help> | |
| 16 </param> | |
| 17 <param name="compound_table" type="data" format="csv,parquet"> | |
| 18 <label>Compound database</label> | |
| 19 <help><![CDATA[ | |
| 20 Database of compounds according to which the annotation is performed. | |
| 21 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>. | |
| 22 ]]></help> | |
| 23 </param> | |
| 24 <param name="adduct_table" type="data" format="csv,parquet" optional="true"> | |
| 25 <label>Adduct database (optional)</label> | |
| 26 <help><![CDATA[ | |
| 27 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs. | |
| 28 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>. | |
| 29 ]]></help> | |
| 30 </param> | |
| 31 </xml> | |
| 32 | |
| 33 <xml name="outputs"> | |
| 34 <data name="annotation_parquet" format="parquet"/> | |
| 35 </xml> | |
| 36 | |
| 37 <xml name="tolerance"> | |
| 38 <param name="mass_tolerance_ppm" type="integer" min="0" value="5"> | |
| 39 <label>Mass tolerance [ppm]</label> | |
| 40 <help>Mass tolerance in ppm for database matching.</help> | |
| 41 </param> | |
| 42 <yield/> | |
| 43 </xml> | |
| 44 <token name="@HELP@"> | |
| 45 <![CDATA[ | |
| 46 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database | |
| 47 using advanced methods. | |
| 48 | |
| 49 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured | |
| 50 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are | |
| 51 withing some tolerance. | |
| 52 ]]> | |
| 53 </token> | |
| 54 <xml name="citations"> | |
| 55 <citation type="doi">10.1021/acs.analchem.6b01214</citation> | |
| 56 </xml> | |
| 57 </macros> |