Mercurial > repos > recetox > retip_train
diff macros.xml @ 8:e7771b3d6a40 draft default tip
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author | recetox |
---|---|
date | Fri, 28 Jan 2022 16:29:45 +0000 |
parents | 9012a9dba1db |
children |
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--- a/macros.xml Tue Mar 09 18:31:08 2021 +0000 +++ b/macros.xml Fri Jan 28 16:29:45 2022 +0000 @@ -1,5 +1,25 @@ <macros> <token name="@TOOL_VERSION@">0.5.4</token> + + <xml name="creator"> + <creator> + <person + givenName="Muhammad" + familyName="Usman" + url="https://github.com/smartx-usman" + identifier="0000-0002-9598-0704" /> + <person + givenName="Aleš" + familyName="Křenek" + url="https://github.com/ljocha" + identifier="0000-0002-3395-3196" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI" /> + </creator> + </xml> + <xml name="requirements"> <requirements> <container type="docker">recetox/retip:@TOOL_VERSION@-recetox4</container> @@ -11,27 +31,27 @@ </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: + **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 + - 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. + Retip also includes useful biochemical databases like: BMDB, ChEBI, DrugBank, ECMDB, FooDB, HMDB, KNApSAcK, + PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF. -**Get started** + **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. + 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>