Mercurial > repos > recetox > xmsannotator_advanced
comparison xmsannotator_advanced.xml @ 1:477d579f475b draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit f92295d389582c7aefc9ad82762248ba1058a667"
| author | recetox |
|---|---|
| date | Thu, 24 Sep 2020 07:23:25 +0000 |
| parents | 60aec5c0e1ea |
| children | 3bdef6d114fd |
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| 0:60aec5c0e1ea | 1:477d579f475b |
|---|---|
| 3 <import>xmsannotator_macros.xml</import> | 3 <import>xmsannotator_macros.xml</import> |
| 4 </macros> | 4 </macros> |
| 5 | 5 |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 | 7 |
| 8 <command detect_errors="aggressive"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #set expected_adducts = ['"{}"'.format($i.adduct) for $i in $scoring.expected_adducts] | 9 #set expected_adducts = ['"{}"'.format($i.adduct) for $i in $scoring.expected_adducts] |
| 10 #set expected_adducts = "c(" + ', '.join($expected_adducts) + ")" | 10 #set expected_adducts = "c(" + ', '.join($expected_adducts) + ")" |
| 11 | 11 |
| 12 Rscript -e 'annotation <- xmsannotator::advanced_annotation( | 12 Rscript -e 'annotation <- xmsannotator::advanced_annotation( |
| 13 peaks = rhdf5::h5read("$peaks", "peaks"), | 13 peaks = rhdf5::h5read("$peaks", "peaks"), |