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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 880667785eed143b5d777010c79a12a53a00af4f"
author recetox
date Fri, 09 Oct 2020 08:54:34 +0000
parents 679229b50d4d
children d59ce34543a4
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190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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1 <macros>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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2 <token name="@TOOL_VERSION@">0.5.4</token>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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3 <xml name="requirements">
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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4 <requirements>
3
cb939f736490 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 880667785eed143b5d777010c79a12a53a00af4f"
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5 <container type="docker">recetox/retip:@TOOL_VERSION@-recetox2</container>
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190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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6 </requirements>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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7 </xml>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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8 <xml name="citations">
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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9 <citations>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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10 <citation type="doi">https://doi.org/10.1021/acs.analchem.9b05765</citation>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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11 </citations>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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12 </xml>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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13 <token name="@HELP@"><![CDATA[
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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14 Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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15 chromatography (HPLC) Mass Spectrometry analysis. Retention time calculation can be useful in identifying
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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16 unknowns and removing false positive annotations. It uses five different machine learning algorithms to built a
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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17 stable, accurate and fast RT prediction model:
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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19 - Random Forest: a decision tree algorithms
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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20 - BRNN: Bayesian Regularized Neural Network
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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21 - XGBoost: an extreme Gradient Boosting for tree algorithms
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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22 - lightGBM: a gradient boosting framework that uses tree based learning algorithms.
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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23 - Keras: a high-level neural networks API for Tensorflow
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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25 Retip also includes useful biochemical databases like: BMDB, ChEBI, DrugBank, ECMDB, FooDB, HMDB, KNApSAcK,
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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26 PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF.
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190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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28 **Get started**
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29
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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30 To use Retip, a user needs to prepare a compound retention time library. The input file
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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31 needs compound Name, InChiKey, SMILES code and experimental retention time information for each compound.
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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32 The input must be a CSV file. Retip will use this input file to build a the model and will predict
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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33 retention times for other biochemical databases or an input query list of compounds. It is suggested that
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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34 the file has at least 300 compounds to build a good retention time prediction model.
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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35 ]]>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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36 </token>
190407e59fa4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
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37 </macros>