diff --git a/tools/retip/.shed.yml b/tools/retip/.shed.yml new file mode 100644 index 00000000..c23ac1ee --- /dev/null +++ b/tools/retip/.shed.yml @@ -0,0 +1,16 @@ +categories: + - Metabolomics +owner: "recetox" +remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/retip" +homepage_url: "https://github.com/PaoloBnn/Retip" +type: unrestricted +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "The tool {{ tool_name }} from the Retip tool suite." +suite: + name: "suite_retip" + description: "A suite of Retip (Retention Time Prediction for metabolomics) tools." + long_description: | + "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. diff --git a/tools/retip/macros.xml b/tools/retip/macros.xml new file mode 100644 index 00000000..38beaa56 --- /dev/null +++ b/tools/retip/macros.xml @@ -0,0 +1,37 @@ + + 0.5.4 + + + recetox/retip:@TOOL_VERSION@-recetox0 + + + + + https://doi.org/10.1021/acs.analchem.9b05765 + + + + + diff --git a/tools/retip/retip_apply.xml b/tools/retip/retip_apply.xml new file mode 100644 index 00000000..11170129 --- /dev/null +++ b/tools/retip/retip_apply.xml @@ -0,0 +1,37 @@ + + is retention time predictor for Metabolomics + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tools/retip/retip_descriptors.xml b/tools/retip/retip_descriptors.xml new file mode 100644 index 00000000..72ad83ca --- /dev/null +++ b/tools/retip/retip_descriptors.xml @@ -0,0 +1,33 @@ + + for retention time prediction + + macros.xml + + + + + + + + + + + + + + + + + + + + diff --git a/tools/retip/retip_train.xml b/tools/retip/retip_train.xml new file mode 100644 index 00000000..9e108ab5 --- /dev/null +++ b/tools/retip/retip_train.xml @@ -0,0 +1,33 @@ + + the Keras model to predict retention times + + macros.xml + + + + + + + + + + + + + + + + + + + + diff --git a/tools/retip/test-data/compounds-small.tsv b/tools/retip/test-data/compounds-small.tsv new file mode 100644 index 00000000..d3de58e2 --- /dev/null +++ b/tools/retip/test-data/compounds-small.tsv @@ -0,0 +1,80 @@ +Name InChIKey SMILES RT +Withanone FAZIYUIDUNHZRG-UHFFFAOYNA-N CC(C1CC(C)=C(C)C(=O)O1)C1(O)CCC2C3C4OC4C4(O)CC=CC(=O)C4(C)C3CCC12C 6.82 +Corosolic acid HFGSQOYIOKBQOW-UHFFFAOYNA-N CC1CCC2(CCC3(C)C(=CCC4C5(C)CC(O)C(O)C(C)(C)C5CCC34C)C2C1C)C(O)=O 9.89 +Maslinic acid MDZKJHQSJHYOHJ-UHFFFAOYNA-N CC1(C)CCC2(CCC3(C)C(=CCC4C5(C)CC(O)C(O)C(C)(C)C5CCC34C)C2C1)C(O)=O 9.77 +Soyasapogenol A CDDWAYFUFNQLRZ-UHFFFAOYNA-N CC1(C)CC2C3=CCC4C5(C)CCC(O)C(C)(CO)C5CCC4(C)C3(C)CCC2(C)C(O)C1O 8.94 +Ginsenoside Rh3 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