Mercurial > repos > recetox > retip_train

annotate macros.xml @ 6:9012a9dba1db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 683f472a44f296d65cf572a5e720839fc4c0141e-dirty"
author recetox
date Fri, 05 Mar 2021 15:16:44 +0000
parents eb109d896eb1
children e7771b3d6a40
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
1 <macros>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
2 <token name="@TOOL_VERSION@">0.5.4</token>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
3 <xml name="requirements">
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
4 <requirements>
6
9012a9dba1db "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 683f472a44f296d65cf572a5e720839fc4c0141e-dirty"
recetox
parents: 5
diff changeset
5 <container type="docker">recetox/retip:@TOOL_VERSION@-recetox4</container>
0
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
6 </requirements>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
7 </xml>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
8 <xml name="citations">
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
9 <citations>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
10 <citation type="doi">https://doi.org/10.1021/acs.analchem.9b05765</citation>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
11 </citations>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
12 </xml>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
13 <token name="@HELP@"><![CDATA[
4
948eccfaa9de "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit d989bc22c6af869b77be6a366935d4d7a57cf29d"
recetox
parents: 3
diff changeset
14 **Retip** is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid
0
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
15 chromatography (HPLC) Mass Spectrometry analysis. Retention time calculation can be useful in identifying
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
16 unknowns and removing false positive annotations. It uses five different machine learning algorithms to built a
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
17 stable, accurate and fast RT prediction model:
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
18
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
19 - Random Forest: a decision tree algorithms
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
20 - BRNN: Bayesian Regularized Neural Network
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
21 - XGBoost: an extreme Gradient Boosting for tree algorithms
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
22 - lightGBM: a gradient boosting framework that uses tree based learning algorithms.
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
23 - Keras: a high-level neural networks API for Tensorflow
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
24
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
25 Retip also includes useful biochemical databases like: BMDB, ChEBI, DrugBank, ECMDB, FooDB, HMDB, KNApSAcK,
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
26 PlantCyc, SMPDB, T3DB, UNPD, YMDB and STOFF.
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
27
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
28 **Get started**
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
29
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
30 To use Retip, a user needs to prepare a compound retention time library. The input file
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
31 needs compound Name, InChiKey, SMILES code and experimental retention time information for each compound.
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
32 The input must be a CSV file. Retip will use this input file to build a the model and will predict
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
33 retention times for other biochemical databases or an input query list of compounds. It is suggested that
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
34 the file has at least 300 compounds to build a good retention time prediction model.
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
35 ]]>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
36 </token>
baa7c8768036 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 931ccc430a2b20eebd174d29b45bf3fa18e85f58"
recetox
parents:
diff changeset
37 </macros>