Mercurial > repos > recetox > recetox_xmsannotator_simple
comparison recetox_xmsannotator_simple.xml @ 0:4cf6d71da794 draft
"planemo upload commit 5d3c80fb59c7d68a3d4ae26119821bc8d6fd65f2-dirty"
| author | recetox |
|---|---|
| date | Tue, 25 Aug 2020 11:45:18 +0000 |
| parents | |
| children | fa85bd6fd713 |
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| -1:000000000000 | 0:4cf6d71da794 |
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| 1 <tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="deployment"> | |
| 2 <macros> | |
| 3 <import>recetox_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 data = arrow::read_feather("$peaks"), | |
| 11 metabolites = rhdf5::h5read("$metabolites", "metabolites"), | |
| 12 mz_tolerance_ppm = as.double($mz_tolerance) | |
| 13 )' | |
| 14 -e 'arrow::write_feather(annotation, "$annotation")' | |
| 15 ]]></command> | |
| 16 | |
| 17 <inputs> | |
| 18 <expand macro="peaks"/> | |
| 19 <expand macro="metabolites"/> | |
| 20 <expand macro="mz_tolerance"/> | |
| 21 </inputs> | |
| 22 | |
| 23 <outputs> | |
| 24 <expand macro="annotation_output"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <help><![CDATA[]]></help> | |
| 28 <expand macro="citations"/> | |
| 29 </tool> |