Mercurial > repos > recetox > retip_apply
diff macros.xml @ 0:190407e59fa4 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
author | recetox |
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date | Wed, 30 Sep 2020 09:56:37 +0000 |
parents | |
children | 679229b50d4d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Sep 30 09:56:37 2020 +0000 @@ -0,0 +1,37 @@ +<macros> + <token name="@TOOL_VERSION@">0.5.4</token> + <xml name="requirements"> + <requirements> + <container type="docker">recetox/retip:@TOOL_VERSION@-recetox0</container> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">https://doi.org/10.1021/acs.analchem.9b05765</citation> + </citations> + </xml> + <token name="@HELP@"><![CDATA[ +Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid +chromatography (HPLC) Mass Spectrometry analysis. Retention time calculation can be useful in identifying +unknowns and removing false positive annotations. It uses five different machine learning algorithms to built a +stable, accurate and fast RT prediction model: + +- Random Forest: a decision tree algorithms +- BRNN: Bayesian Regularized Neural Network +- XGBoost: an extreme Gradient Boosting for tree algorithms +- lightGBM: a gradient boosting framework that uses tree based learning algorithms. +- Keras: a high-level neural networks API for Tensorflow + +Retip also includes useful biochemical databases like: BMDB, ChEBI, DrugBank, ECMDB, FooDB, HMDB, KNApSAcK, +PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF. + +**Get started** + +To use Retip, a user needs to prepare a compound retention time library. The input file +needs compound Name, InChiKey, SMILES code and experimental retention time information for each compound. +The input must be a CSV file. Retip will use this input file to build a the model and will predict +retention times for other biochemical databases or an input query list of compounds. It is suggested that +the file has at least 300 compounds to build a good retention time prediction model. + ]]> + </token> +</macros>