Mercurial > repos > recetox > xmsannotator_simple
comparison xmsannotator_simple.xml @ 0:97d1619ff23e draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
| author | recetox |
|---|---|
| date | Wed, 23 Sep 2020 13:31:39 +0000 |
| parents | |
| children | 041052875af0 |
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| -1:000000000000 | 0:97d1619ff23e |
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| 1 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0"> | |
| 2 <macros> | |
| 3 <import>xmsannotator_macros.xml</import> | |
| 4 </macros> | |
| 5 | |
| 6 <expand macro="requirements"/> | |
| 7 | |
| 8 <command detect_errors="aggressive"><![CDATA[ | |
| 9 Rscript -e 'annotation <- xmsannotator::simple_annotation( | |
| 10 peaks = rhdf5::h5read("$peaks", "peaks"), | |
| 11 adducts = rhdf5::h5read("$adducts", "adducts"), | |
| 12 metabolites = rhdf5::h5read("$metabolites", "metabolites"), | |
| 13 mz_tolerance_ppm = as.double($mz_tolerance_ppm) | |
| 14 )' | |
| 15 -e 'rhdf5::h5write(annotation, "$annotation", "annotation")' | |
| 16 ]]></command> | |
| 17 | |
| 18 <inputs> | |
| 19 <expand macro="annotation"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <expand macro="output"/> | |
| 23 </outputs> | |
| 24 | |
| 25 <help><![CDATA[ | |
| 26 Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database. | |
| 27 | |
| 28 The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks. | |
| 29 A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance. | |
| 30 ]]></help> | |
| 31 <expand macro="citations"/> | |
| 32 </tool> |