From b05daf1c20edcace7f01405e6974d33f43aa1576 Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 7 Nov 2024 16:32:48 +0100 Subject: [PATCH 1/9] scipy interpolate tool initial commit --- tools/scipy/.shed.yml | 16 ++++++ tools/scipy/scipy_interpolate.xml | 77 +++++++++++++++++++++++++++++ tools/scipy/test-data/reference.txt | 29 +++++++++++ 3 files changed, 122 insertions(+) create mode 100644 tools/scipy/.shed.yml create mode 100644 tools/scipy/scipy_interpolate.xml create mode 100644 tools/scipy/test-data/reference.txt diff --git a/tools/scipy/.shed.yml b/tools/scipy/.shed.yml new file mode 100644 index 00000000..313737d9 --- /dev/null +++ b/tools/scipy/.shed.yml @@ -0,0 +1,16 @@ +name: scipy +owner: recetox +remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/scipy" +homepage_url: "https://docs.scipy.org/doc/scipy/tutorial/interpolate.html" +categories: + - Metabolomics + - Statistics +description: "Searching, filtering and converting mass spectral libraries." +long_description: "Tools to filter (normalize intensities, filter mz range, convert adducts, ...) and convert (msp/mgf/json) mass spectral libraries and to perform spectral, fingerprint and metadata similarity calculations as well as molecular networking." +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "{{ tool_name }} tool from the scipy package" +suite: + name: suite_scipy + description: tools from the scipy suite are used for science + type: repository_suite_definition \ No newline at end of file diff --git a/tools/scipy/scipy_interpolate.xml b/tools/scipy/scipy_interpolate.xml new file mode 100644 index 00000000..610416dd --- /dev/null +++ b/tools/scipy/scipy_interpolate.xml @@ -0,0 +1,77 @@ + + interpolate data using the scipy.interpolate library + + + 1.14.1 + 0 + + + + + + scipy + pandas + + + + +import pandas as pd +from scipy.interpolate import CubicSpline, PchipInterpolator, Akima1DInterpolator +import numpy as np + +reference = pd.read_csv('$reference_dataset', sep='\t') +query = pd.read_csv('$query_dataset', sep='\t') + +model = ${method}(reference['RI'], reference['RT']) +query['RT'] = model(query['retention_index']).astype(float) +query.to_csv('$output_dataset', sep='\t', index=False) + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/tools/scipy/test-data/reference.txt b/tools/scipy/test-data/reference.txt new file mode 100644 index 00000000..49c22148 --- /dev/null +++ b/tools/scipy/test-data/reference.txt @@ -0,0 +1,29 @@ +RI RT +1300 2.9 +1400 3.2 +1500 3.6 +1600 4.1 +1700 4.5 +1800 4.9 +1900 5.3 +2000 5.7 +2100 6.0 +2200 6.3 +2300 6.6 +2400 6.9 +2500 7.2 +2600 7.4 +2700 7.6 +2800 7.8 +2900 8.1 +3000 8.3 +3100 8.5 +3200 8.8 +3300 9.2 +3400 9.5 +3500 9.9 +3600 10.4 +3700 11.0 +3800 11.7 +3900 12.0 +4000 12.5 \ No newline at end of file From a7a24d52b8e22152489e2e468c49139a7655b837 Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 14 Nov 2024 14:48:26 +0100 Subject: [PATCH 2/9] starting table tool implementation --- tools/scipy/pandas_arithmetics.py | 36 ++++++++++++++++++++++ tools/scipy/pandas_arithmetics.xml | 43 ++++++++++++++++++++++++++ tools/scipy/scipy_interpolate.py | 46 ++++++++++++++++++++++++++++ tools/scipy/scipy_interpolate.xml | 49 ++++++++++++++++-------------- tools/scipy/utils.py | 39 ++++++++++++++++++++++++ 5 files changed, 190 insertions(+), 23 deletions(-) create mode 100644 tools/scipy/pandas_arithmetics.py create mode 100644 tools/scipy/pandas_arithmetics.xml create mode 100644 tools/scipy/scipy_interpolate.py create mode 100644 tools/scipy/utils.py diff --git a/tools/scipy/pandas_arithmetics.py b/tools/scipy/pandas_arithmetics.py new file mode 100644 index 00000000..bffa5f5f --- /dev/null +++ b/tools/scipy/pandas_arithmetics.py @@ -0,0 +1,36 @@ +import argparse + +from utils import LoadDataAction, StoreOutputAction + +def perform_operation(df, column_index, operation, operand): + column_name = df.columns[column_index - 1] # Convert base-1 index to zero-based index + if operation == 'mul': + df[column_name] = df[column_name] * operand + elif operation == 'sub': + df[column_name] = df[column_name] - operand + elif operation == 'div': + df[column_name] = df[column_name] / operand + elif operation == 'add': + df[column_name] = df[column_name] + operand + elif operation == 'pow': + df[column_name] = df[column_name] ** operand + else: + raise ValueError(f"Unsupported operation: {operation}") + return df + +def main(input_dataset, column_index, operation, operand, output_dataset): + df = input_dataset + df = perform_operation(df, column_index, operation, operand) + write_func, file_path = output_dataset + write_func(df, file_path) + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Perform arithmetic operations on a dataframe column.') + parser.add_argument('--input_dataset', nargs=2, action=LoadDataAction, required=True, help='Path to the input dataset and its file extension (csv, tsv, parquet)') + parser.add_argument('--column', type=int, required=True, help='Base-1 index of the column to perform the operation on') + parser.add_argument('--operation', type=str, choices=['mul', 'sub', 'div', 'add', 'pow'], required=True, help='Arithmetic operation to perform') + parser.add_argument('--operand', type=float, required=True, help='Operand for the arithmetic operation') + parser.add_argument('--output_dataset', nargs=2, action=StoreOutputAction, required=True, help='Path to the output dataset and its file extension (csv, tsv, parquet)') + + args = parser.parse_args() + main(args.input_dataset, args.column, args.operation, args.operand, args.output_dataset) \ No newline at end of file diff --git a/tools/scipy/pandas_arithmetics.xml b/tools/scipy/pandas_arithmetics.xml new file mode 100644 index 00000000..7198ad1c --- /dev/null +++ b/tools/scipy/pandas_arithmetics.xml @@ -0,0 +1,43 @@ + + perform arithmetic operations on a dataframe column + + 2.2.3 + 0 + + + pandas + pyarrow + + + + + + + + + + + + + + + + + + + + + + + + This tool performs arithmetic operations on a specified column of a dataframe. + Supported operations are: multiply, subtract, divide, add, and power. + + \ No newline at end of file diff --git a/tools/scipy/scipy_interpolate.py b/tools/scipy/scipy_interpolate.py new file mode 100644 index 00000000..c36ae26a --- /dev/null +++ b/tools/scipy/scipy_interpolate.py @@ -0,0 +1,46 @@ +import argparse +import numpy as np +from scipy.interpolate import CubicSpline, PchipInterpolator, Akima1DInterpolator + +from utils import LoadDataAction, StoreOutputAction + +class InterpolationModelAction(argparse.Action): + def __call__(self, parser, namespace, values, option_string=None): + interpolators = { + "linear": np.interp, + "cubic": CubicSpline, + "pchip": PchipInterpolator, + "akima": Akima1DInterpolator + } + if values not in interpolators: + raise ValueError(f"Unknown interpolation method: {values}") + setattr(namespace, self.dest, interpolators[values]) + + +def main(reference, query, x_col, y_col, xnew_col, model, output_dataset): + # Index is passed with base 1 so we need to subtract 1 to get the correct column names + x_col = reference.columns[x_col - 1] + y_col = reference.columns[y_col - 1] + xnew_col = query.columns[xnew_col - 1] + + if model == np.interp: + query[y_col] = model(query[xnew_col], reference[x_col], reference[y_col]) + else: + model_instance = model(reference[x_col], reference[y_col]) + query[y_col] = model_instance(query[xnew_col]).astype(float) + + write_func, file_path = output_dataset + write_func(query, file_path) + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='Interpolate data using various methods.') + parser.add_argument('--reference_dataset', nargs=2, action=LoadDataAction, required=True, help='Path to the reference dataset and its file extension (csv, tsv, parquet)') + parser.add_argument('--query_dataset', nargs=2, action=LoadDataAction, required=True, help='Path to the query dataset and its file extension (csv, tsv, parquet)') + parser.add_argument('--x_col', type=int, required=True, help='Index of the x column in the reference dataset (1-based)') + parser.add_argument('--y_col', type=int, required=True, help='Index of the y column in the reference dataset (1-based)') + parser.add_argument('--xnew_col', type=int, required=True, help='Index of the x column in the query dataset (1-based)') + parser.add_argument('--method', type=str, choices=['linear', 'cubic', 'pchip', 'akima'], action=InterpolationModelAction, required=True, help='Interpolation method') + parser.add_argument('--output_dataset', nargs=2, action=StoreOutputAction, required=True, help='Path to the output dataset and its file extension (csv, tsv, parquet)') + + args = parser.parse_args() + main(args.reference_dataset, args.query_dataset, args.x_col, args.y_col, args.xnew_col, args.method, args.output_dataset) \ No newline at end of file diff --git a/tools/scipy/scipy_interpolate.xml b/tools/scipy/scipy_interpolate.xml index 610416dd..fb82e564 100644 --- a/tools/scipy/scipy_interpolate.xml +++ b/tools/scipy/scipy_interpolate.xml @@ -18,36 +18,39 @@ scipy pandas + pyarrow - - -import pandas as pd -from scipy.interpolate import CubicSpline, PchipInterpolator, Akima1DInterpolator -import numpy as np - -reference = pd.read_csv('$reference_dataset', sep='\t') -query = pd.read_csv('$query_dataset', sep='\t') - -model = ${method}(reference['RI'], reference['RT']) -query['RT'] = model(query['retention_index']).astype(float) -query.to_csv('$output_dataset', sep='\t', index=False) - - - - - - - - + + + + + + + + + + + - + + + + + @@ -62,7 +65,7 @@ TODO: Fill in help in reStructuredText format (https://docutils.sourceforge.io/d Usage ..... - +[1] (https://docs.scipy.org/doc/scipy/tutorial/interpolate.html) **Input** diff --git a/tools/scipy/utils.py b/tools/scipy/utils.py new file mode 100644 index 00000000..46209214 --- /dev/null +++ b/tools/scipy/utils.py @@ -0,0 +1,39 @@ +import argparse +import pandas as pd + +class LoadDataAction(argparse.Action): + def __call__(self, parser, namespace, values, option_string=None): + file_path, file_extension = values + file_extension = file_extension.lower() + if file_extension == 'csv': + df = pd.read_csv(file_path) + elif file_extension in ['tsv', 'tabular']: + df = pd.read_csv(file_path, sep='\t') + elif file_extension == 'parquet': + df = pd.read_parquet(file_path) + else: + raise ValueError(f"Unsupported file format: {file_extension}") + setattr(namespace, self.dest, df) + +def write_csv(df, file_path): + df.to_csv(file_path, index=False) + +def write_tsv(df, file_path): + df.to_csv(file_path, sep='\t', index=False) + +def write_parquet(df, file_path): + df.to_parquet(file_path, index=False) + +class StoreOutputAction(argparse.Action): + def __call__(self, parser, namespace, values, option_string=None): + file_path, file_extension = values + file_extension = file_extension.lower() + if file_extension == 'csv': + write_func = write_csv + elif file_extension in ['tsv', 'tabular']: + write_func = write_tsv + elif file_extension == 'parquet': + write_func = write_parquet + else: + raise ValueError(f"Unsupported file format: {file_extension}") + setattr(namespace, self.dest, (write_func, file_path)) \ No newline at end of file From 54f15570885efed6df3bd1cbab698ae871161fe2 Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 14 Nov 2024 16:10:22 +0100 Subject: [PATCH 3/9] renamed toolbox to analysis --- tools/analysis/.shed.yml | 16 ++ .../analysis_pandas_arithmetics.py} | 0 .../analysis_pandas_arithmetics.xml} | 4 + .../analysis_scipy_interpolate.py} | 0 .../analysis_scipy_interpolate.xml} | 3 +- tools/analysis/test-data/query.tabular | 266 ++++++++++++++++++ .../test-data/reference.txt | 0 tools/{scipy => analysis}/utils.py | 0 tools/scipy/.shed.yml | 16 -- 9 files changed, 288 insertions(+), 17 deletions(-) create mode 100644 tools/analysis/.shed.yml rename tools/{scipy/pandas_arithmetics.py => analysis/analysis_pandas_arithmetics.py} (100%) rename tools/{scipy/pandas_arithmetics.xml => analysis/analysis_pandas_arithmetics.xml} (92%) rename tools/{scipy/scipy_interpolate.py => analysis/analysis_scipy_interpolate.py} (100%) rename tools/{scipy/scipy_interpolate.xml => analysis/analysis_scipy_interpolate.xml} (96%) create mode 100644 tools/analysis/test-data/query.tabular rename tools/{scipy => analysis}/test-data/reference.txt (100%) rename tools/{scipy => analysis}/utils.py (100%) delete mode 100644 tools/scipy/.shed.yml diff --git a/tools/analysis/.shed.yml b/tools/analysis/.shed.yml new file mode 100644 index 00000000..4a0e1f89 --- /dev/null +++ b/tools/analysis/.shed.yml @@ -0,0 +1,16 @@ +name: analysis +owner: recetox +remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/analysis" +homepage_url: "https://github.com/RECETOX/galaxytools" +categories: + - Metabolomics + - Statistics +description: "Tools to manipulate and analyze data tables." +long_description: "Tools to manipulate and analyze data tables. Current tools include interpolation using scipy and arithmetic operations on tables with pandas." +auto_tool_repositories: + name_template: "{{ tool_id }}" + description_template: "{{ tool_name }} tool from the general purpose data analysis suite developed by RECETOX." +suite: + name: suite_analysis + description: This tool suites contains tools for general purpose data analysis built on top of pandas, scipy, dplyr and others. + type: repository_suite_definition \ No newline at end of file diff --git a/tools/scipy/pandas_arithmetics.py b/tools/analysis/analysis_pandas_arithmetics.py similarity index 100% rename from tools/scipy/pandas_arithmetics.py rename to tools/analysis/analysis_pandas_arithmetics.py diff --git a/tools/scipy/pandas_arithmetics.xml b/tools/analysis/analysis_pandas_arithmetics.xml similarity index 92% rename from tools/scipy/pandas_arithmetics.xml rename to tools/analysis/analysis_pandas_arithmetics.xml index 7198ad1c..544c85d3 100644 --- a/tools/scipy/pandas_arithmetics.xml +++ b/tools/analysis/analysis_pandas_arithmetics.xml @@ -40,4 +40,8 @@ This tool performs arithmetic operations on a specified column of a dataframe. Supported operations are: multiply, subtract, divide, add, and power. + + 10.5281/zenodo.3509134 + 10.25080/Majora-92bf1922-00a + \ No newline at end of file diff --git a/tools/scipy/scipy_interpolate.py b/tools/analysis/analysis_scipy_interpolate.py similarity index 100% rename from tools/scipy/scipy_interpolate.py rename to tools/analysis/analysis_scipy_interpolate.py diff --git a/tools/scipy/scipy_interpolate.xml b/tools/analysis/analysis_scipy_interpolate.xml similarity index 96% rename from tools/scipy/scipy_interpolate.xml rename to tools/analysis/analysis_scipy_interpolate.xml index fb82e564..d4ff35a4 100644 --- a/tools/scipy/scipy_interpolate.xml +++ b/tools/analysis/analysis_scipy_interpolate.xml @@ -75,6 +75,7 @@ Usage ]]> - + 10.25080/Majora-92bf1922-00a + 10.1038/s41592-019-0686-2 \ No newline at end of file diff --git a/tools/analysis/test-data/query.tabular b/tools/analysis/test-data/query.tabular new file mode 100644 index 00000000..aeddc4a8 --- /dev/null +++ b/tools/analysis/test-data/query.tabular @@ -0,0 +1,266 @@ +precursor_mz license retention_index authors compound_name +362.18381 CC BY-NC 2520.736 Price et al., RECETOX, Masaryk University (CZ) Acetylserotonin_2TMS isomer 2 +489.1889 CC BY-NC 2566.364 Price et al., RECETOX, Masaryk University (CZ) Acetylserotonin_TMS derivative +434.22321 CC BY-NC 2415.476 Price et al., RECETOX, Masaryk University (CZ) Acetylserotonin_3TMS +362.18381 CC BY-NC 2475.613 Price et al., RECETOX, Masaryk University (CZ) Acetylserotonin_2TMS isomer 1 +136.05856 CC BY-NC 1443.328 Price et al., RECETOX, Masaryk University (CZ) Methylnicotinamide +261.06659 CC BY-NC 1376.073 Price et al., RECETOX, Masaryk University (CZ) Pipecolinic acid_2TMS +201.11786 CC BY-NC 1292.953 Price et al., RECETOX, Masaryk University (CZ) Pipecolinic acid_1TMS +194.06293 CC BY-NC 1316.816 Price et al., RECETOX, Masaryk University (CZ) Nicotinic acid_1TMS +362.16293 CC BY-NC 1664.769 Price et al., RECETOX, Masaryk University (CZ) Ribose_4TMS +342.13101 CC BY-NC 1892.004 Price et al., RECETOX, Masaryk University (CZ) Syringic acid_2TMS +367.16711 CC BY-NC 2118.982 Price et al., RECETOX, Masaryk University (CZ) Guanine_3TMS +439.20303 CC BY-NC 2175.041 Price et al., RECETOX, Masaryk University (CZ) Guanine_4TMS +260.14963 CC BY-NC 1282.975 Price et al., RECETOX, Masaryk University (CZ) Leucine_2TMS +458.17902 CC BY-NC 1951.021 Price et al., RECETOX, Masaryk University (CZ) Gallic acid_4TMS +396.16028 CC BY-NC 2131.329 Price et al., RECETOX, Masaryk University (CZ) trans-Caffeic acid_3TMS +396.1604 CC BY-NC 1975.29 Price et al., RECETOX, Masaryk University (CZ) cis-Caffeic acid_3TMS +525.24902 CC BY-NC 2071.766 Price et al., RECETOX, Masaryk University (CZ) Acetylglucosamine_5TMS isomer 1 +579.297 CC BY-NC 2081.004 Price et al., RECETOX, Masaryk University (CZ) Acetylglucosamine_5TMS isomer 2 +326.1362 CC BY-NC 1761.149 Price et al., RECETOX, Masaryk University (CZ) 4-Hydroxy-3methoxyphenylacetic acid_2TMS +278.12305 CC BY-NC 1317.247 Price et al., RECETOX, Masaryk University (CZ) Glycine_3TMS +270.12137 CC BY-NC 1402.643 Price et al., RECETOX, Masaryk University (CZ) Thymine_2TMS +348.1713 CC BY-NC 1658.764 Price et al., RECETOX, Masaryk University (CZ) Asparagine_3TMS +368.1339 CC BY-NC 1499.852 Price et al., RECETOX, Masaryk University (CZ) Asparagine_2TMS +420.21198 CC BY-NC 1598.743 Price et al., RECETOX, Masaryk University (CZ) Asparagine_4TMS isomer 1 +420.21072 CC BY-NC 1619.979 Price et al., RECETOX, Masaryk University (CZ) Asparagine_4TMS isomer 2 +320.15897 CC BY-NC 1782.981 Price et al., RECETOX, Masaryk University (CZ) Azelaic acid_2TMS +319.14154 CC BY-NC 1960.418 Price et al., RECETOX, Masaryk University (CZ) Indole-3-acetic acid_2TMS +245.10255 CC BY-NC 1919.926 Price et al., RECETOX, Masaryk University (CZ) Indole-3-acetic acid_1TMS +355.1398 CC BY-NC 2119.143 Price et al., RECETOX, Masaryk University (CZ) Acetyltyrosine_2TMS +426.17551 CC BY-NC 2085.942 Price et al., RECETOX, Masaryk University (CZ) Acetyltyrosine_3TMS +518.24091 CC BY-NC 1900.622 Price et al., RECETOX, Masaryk University (CZ) Allantoin_5TMS +446.20102 CC BY-NC 1877.684 Price et al., RECETOX, Masaryk University (CZ) Allantoin_4TMS +374.16168 CC BY-NC 2065.527 Price et al., RECETOX, Masaryk University (CZ) Allantoin_3TMS +252.10365 CC BY-NC 1988.727 Price et al., RECETOX, Masaryk University (CZ) Theobromine_1TMS +473.1601 CC BY-NC 2310.707 Price et al., RECETOX, Masaryk University (CZ) Glucose-6-phosphate_6TMS isomer 1 +472.16409 CC BY-NC 2332.412 Price et al., RECETOX, Masaryk University (CZ) Glucose-6-phosphate_6TMS isomer 2 +434.21536 CC BY-NC 1936.412 Price et al., RECETOX, Masaryk University (CZ) Galactitol_6TMS +422.21552 CC BY-NC 1713.998 Price et al., RECETOX, Masaryk University (CZ) Ribitol_5TMS +363.17084 CC BY-NC 1611.723 Price et al., RECETOX, Masaryk University (CZ) Glutamic acid_3TMS spectra 2 +273.12088 CC BY-NC 1519.766 Price et al., RECETOX, Masaryk University (CZ) Pyroglutamic acid_2TMS +285.13287 CC BY-NC 1528.459 Price et al., RECETOX, Masaryk University (CZ) Glutamic acid_2TMS +460.40933 CC BY-NC 3195.161 Price et al., RECETOX, Masaryk University (CZ) Cholestanol_1TMS +249.07844 CC BY-NC 1318.455 Price et al., RECETOX, Masaryk University (CZ) Succinic acid_1TMS +598.29169 CC BY-NC 2734.555 Price et al., RECETOX, Masaryk University (CZ) Maltose_8TMS isomer 1 +624.3072 CC BY-NC 2762.246 Price et al., RECETOX, Masaryk University (CZ) Maltose_8TMS isomer 2 +292.13931 CC BY-NC 1366.752 Price et al., RECETOX, Masaryk University (CZ) Alanine_3TMS +227.02199 CC BY-NC 1133.662 Price et al., RECETOX, Masaryk University (CZ) Alanine_2TMS +232.07872 CC BY-NC 1772.129 Price et al., RECETOX, Masaryk University (CZ) Indole-2-carboxylic acid_1TMS +273.11054 CC BY-NC 1223.943 Price et al., RECETOX, Masaryk University (CZ) Aspartic acid_2TMS +415.03641 CC BY-NC 1722.841 Price et al., RECETOX, Masaryk University (CZ) Aspartic acid_4TMS +300.2475 CC BY-NC 1839.995 Price et al., RECETOX, Masaryk University (CZ) Myristic acid_1TMS +306.13684 CC BY-NC 1512.481 Price et al., RECETOX, Masaryk University (CZ) Aspartic acid_3TMS isomer +333.15714 CC BY-NC 2080.405 Price et al., RECETOX, Masaryk University (CZ) 3-Indolepropionic acid +261.11783 CC BY-NC 2031.59 Price et al., RECETOX, Masaryk University (CZ) 3-Indolepropionic acid_1TMS +305.12579 CC BY-NC 2023.71 Price et al., RECETOX, Masaryk University (CZ) Indole-3-carboxylic acid_2TMS +451.18115 CC BY-NC 1874.721 Price et al., RECETOX, Masaryk University (CZ) Gluconic acid-1,5-lactone +466.20514 CC BY-NC 1888.373 Price et al., RECETOX, Masaryk University (CZ) Gluconic acid-1,4-lactone +614.27368 CC BY-NC 1994.983 Price et al., RECETOX, Masaryk University (CZ) Gluconic acid_6TMS +377.16287 CC BY-NC 1917.593 Price et al., RECETOX, Masaryk University (CZ) Gluconolactone +208.0979 CC BY-NC 1456.937 Price et al., RECETOX, Masaryk University (CZ) Methylnicotinamide_1TMS +466.22858 CC BY-NC 1877.592 Price et al., RECETOX, Masaryk University (CZ) Mannose_5TMS isomer 1 +448.21866 CC BY-NC 1895.569 Price et al., RECETOX, Masaryk University (CZ) Mannose_5TMS isomer 2 +376.19946 CC BY-NC 2384.715 Price et al., RECETOX, Masaryk University (CZ) Melatonin_2TMS +304.15997 CC BY-NC 2445.713 Price et al., RECETOX, Masaryk University (CZ) Melatonin_1TMS +543.21246 CC BY-NC 2564.368 Price et al., RECETOX, Masaryk University (CZ) Inosine_4TMS +242.02328 CC BY-NC 1433.812 Price et al., RECETOX, Masaryk University (CZ) Acetylleucine_1TMS +304.15579 CC BY-NC 1421.252 Price et al., RECETOX, Masaryk University (CZ) Acetylleucine_2TMS +268.11243 CC BY-NC 1708.024 Price et al., RECETOX, Masaryk University (CZ) Homoveratric_acid_1TMS +434.2149 CC BY-NC 1925.111 Price et al., RECETOX, Masaryk University (CZ) Mannitol_6TMS +222.14323 CC BY-NC 1321.728 Price et al., RECETOX, Masaryk University (CZ) Thymol_1TMS +406.18625 CC BY-NC 2212.521 Price et al., RECETOX, Masaryk University (CZ) Tryptophan_3TMS +331.14139 CC BY-NC 2153.768 Price et al., RECETOX, Masaryk University (CZ) Tryptophan_2TMS +378.10901 CC BY-NC 1733.549 Price et al., RECETOX, Masaryk University (CZ) trans-Aconitic acid_3TMS +468.37778 CC BY-NC 3264.982 Price et al., RECETOX, Masaryk University (CZ) Ergosterol_1TMS +277.10928 CC BY-NC 1421.292 Price et al., RECETOX, Masaryk University (CZ) 3-Methylglutaric acid_2TMS +396.19299 CC BY-NC 1707.47 Price et al., RECETOX, Masaryk University (CZ) Arabitol_5TMS +413.3653 CC BY-NC 3300.418 Price et al., RECETOX, Masaryk University (CZ) Cholestenone +434.21451 CC BY-NC 1932.941 Price et al., RECETOX, Masaryk University (CZ) Sorbitol_6TMS +269.13876 CC BY-NC 1299.49 Price et al., RECETOX, Masaryk University (CZ) Isoleucine_2TMS +464.2132 CC BY-NC 1861.884 Price et al., RECETOX, Masaryk University (CZ) Fructose_5TMS isomer 1 +555.26501 CC BY-NC 1871.707 Price et al., RECETOX, Masaryk University (CZ) Fructose_5TMS isomer 2 +249.05966 CC BY-NC 1350.603 Price et al., RECETOX, Masaryk University (CZ) Fumaric acid_2TMS +468.15952 CC BY-NC 1801.269 Price et al., RECETOX, Masaryk University (CZ) Isocitric acid_4TMS +204.09969 CC BY-NC 1246.784 Price et al., RECETOX, Masaryk University (CZ) Urea_2TMS +276.15033 CC BY-NC 1199.655 Price et al., RECETOX, Masaryk University (CZ) Urea_3TMS +643.29096 CC BY-NC 2761.007 Price et al., RECETOX, Masaryk University (CZ) Guanosine_5TMS +371.18732 CC BY-NC 1914.512 Price et al., RECETOX, Masaryk University (CZ) Histidine_3TMS +443.22736 CC BY-NC 2146.867 Price et al., RECETOX, Masaryk University (CZ) Histidine_4TMS +421.19458 CC BY-NC 1640.562 Price et al., RECETOX, Masaryk University (CZ) Xylose_4TMS +190.07045 CC BY-NC 1269.712 Price et al., RECETOX, Masaryk University (CZ) Acetylalanine_1TMS +392.20975 CC BY-NC 1940.186 Price et al., RECETOX, Masaryk University (CZ) Glycylleucine_3TMS +384.16013 CC BY-NC 1815.935 Price et al., RECETOX, Masaryk University (CZ) 3,4-Dihydroxybenzeneacetic acid_3TMS +476.27365 CC BY-NC 1870.232 Price et al., RECETOX, Masaryk University (CZ) Glycylleucine_4TMS +318.15744 CC BY-NC 2098.84 Price et al., RECETOX, Masaryk University (CZ) Indole-3-acetamide_2TMS +389.18936 CC BY-NC 2048.997 Price et al., RECETOX, Masaryk University (CZ) Indole-3-acetamide_3TMS +520.3761 CC BY-NC 3290.675 Price et al., RECETOX, Masaryk University (CZ) Lithocholic acid_2TMS +464.2132 CC BY-NC 1868.664 Price et al., RECETOX, Masaryk University (CZ) Allose_5TMS isomer 1 +402.17654 CC BY-NC 1895.068 Price et al., RECETOX, Masaryk University (CZ) Allose_5TMS isomer 2 +390.23691 CC BY-NC 2274.265 Price et al., RECETOX, Masaryk University (CZ) Tetradecanedioic acid_2TMS +596.39124 CC BY-NC 3706.675 Price et al., RECETOX, Masaryk University (CZ) Deoxycholic acid_3TMS +396.19266 CC BY-NC 1706.712 Price et al., RECETOX, Masaryk University (CZ) Arabitol_5TMS +459.14395 CC BY-NC 1820.179 Price et al., RECETOX, Masaryk University (CZ) Phosphoserine_4TMS +337.11273 CC BY-NC 1479.336 Price et al., RECETOX, Masaryk University (CZ) Malic acid_3TMS +256.10553 CC BY-NC 1340.716 Price et al., RECETOX, Masaryk University (CZ) Uracil_2TMS +555.25403 CC BY-NC 2626.723 Price et al., RECETOX, Masaryk University (CZ) Adenosine_4TMS +627.2951 CC BY-NC 2694.825 Price et al., RECETOX, Masaryk University (CZ) Adenosine_5TMS +324.98636 CC BY-NC 1925.08 Price et al., RECETOX, Masaryk University (CZ) Acetylglutamine_2TMS +476.2366 CC BY-NC 1850.038 Price et al., RECETOX, Masaryk University (CZ) Acetylglutamine_4TMS +308.15137 CC BY-NC 1526.173 Price et al., RECETOX, Masaryk University (CZ) gamma-Aminobutyric acid_3TMS +401.98407 CC BY-NC 1744.992 Price et al., RECETOX, Masaryk University (CZ) Acetylglutamine_3TMS +247.11795 CC BY-NC 1267.765 Price et al., RECETOX, Masaryk University (CZ) gamma-Aminobutyric acid_2TMS +219.10622 CC BY-NC 1160.418 Price et al., RECETOX, Masaryk University (CZ) Sarcosine_2TMS +262.10492 CC BY-NC 1226.577 Price et al., RECETOX, Masaryk University (CZ) 2-Methylmalonic acid_2TMS +273.12122 CC BY-NC 1518.258 Price et al., RECETOX, Masaryk University (CZ) Pyroglutamic acid_2TMS +391.166 CC BY-NC 1654.213 Price et al., RECETOX, Masaryk University (CZ) Acetylaspartic acid_3TMS +330.10126 CC BY-NC 1662.921 Price et al., RECETOX, Masaryk University (CZ) Taurine_3TMS +508.25763 CC BY-NC 2081.314 Price et al., RECETOX, Masaryk University (CZ) Acetylgalactosamine_4TMS +467.15692 CC BY-NC 1800.533 Price et al., RECETOX, Masaryk University (CZ) Citric acid_4TMS +581.29388 CC BY-NC 2068.947 Price et al., RECETOX, Masaryk University (CZ) Acetylgalactosamine_5TMS isomer 1 +372.12848 CC BY-NC 1730.0 Price et al., RECETOX, Masaryk University (CZ) Orotic acid_3TMS +434.20194 CC BY-NC 2091.044 Price et al., RECETOX, Masaryk University (CZ) Acetylgalactosamine_5TMS isomer 2 +373.20316 CC BY-NC 1808.72 Price et al., RECETOX, Masaryk University (CZ) Arginine_3TMS +539.2533 CC BY-NC 3541.85 Price et al., RECETOX, Masaryk University (CZ) Maltotriose_11TMS isomer 1 +648.42804 CC BY-NC 3577.725 Price et al., RECETOX, Masaryk University (CZ) Maltotriose_11TMS isomer 2 +410.17297 CC BY-NC 1548.223 Price et al., RECETOX, Masaryk University (CZ) Threonic acid_4TMS +325.00406 CC BY-NC 1383.911 Price et al., RECETOX, Masaryk University (CZ) Threonine_3TMS spectra 2 +334.17438 CC BY-NC 1884.285 Price et al., RECETOX, Masaryk University (CZ) Sebacid acid_2TMS +312.11047 CC BY-NC 1599.903 Price et al., RECETOX, Masaryk University (CZ) Hypotaurine_3TMS +333.12225 CC BY-NC 2064.473 Price et al., RECETOX, Masaryk University (CZ) Kynurenic acid_2TMS +390.21848 CC BY-NC 1751.486 Price et al., RECETOX, Masaryk University (CZ) Theanine_3TMS +318.1786 CC BY-NC 1767.969 Price et al., RECETOX, Masaryk University (CZ) Theanine_2TMS +311.11298 CC BY-NC 1691.138 Price et al., RECETOX, Masaryk University (CZ) 4-Methoxymandelic acid_2TMS +404.23398 CC BY-NC 2099.177 Price et al., RECETOX, Masaryk University (CZ) Acetyllysine_3TMS +476.27362 CC BY-NC 2062.792 Price et al., RECETOX, Masaryk University (CZ) Acetyllysine_4TMS +298.28644 CC BY-NC 2123.088 Price et al., RECETOX, Masaryk University (CZ) Methyl stearate +334.18509 CC BY-NC 1718.079 Price et al., RECETOX, Masaryk University (CZ) 6-Aminocaproic acid_3TMS +275.17328 CC BY-NC 1489.369 Price et al., RECETOX, Masaryk University (CZ) 6-Aminocaproic acid_2TMS +305.14038 CC BY-NC 1686.939 Price et al., RECETOX, Masaryk University (CZ) Suberic acid_2TMS +234.10721 CC BY-NC 1564.514 Price et al., RECETOX, Masaryk University (CZ) alpha-Methylcinammic acid_1TMS +250.96794 CC BY-NC 1308.31 Price et al., RECETOX, Masaryk University (CZ) Maleic acid_2TMS +334.14865 CC BY-NC 1513.131 Price et al., RECETOX, Masaryk University (CZ) Hydroxyproline_3TMS +498.91568 CC BY-NC 2272.319 Price et al., RECETOX, Masaryk University (CZ) Cystine_4TMS +260.14963 CC BY-NC 1316.851 Price et al., RECETOX, Masaryk University (CZ) Norleucine_2TMS +329.17691 CC BY-NC 1545.214 Price et al., RECETOX, Masaryk University (CZ) Creatinine_3TMS +338.13629 CC BY-NC 2077.594 Price et al., RECETOX, Masaryk University (CZ) Ferulic acid_2TMS +263.09412 CC BY-NC 1396.082 Price et al., RECETOX, Masaryk University (CZ) Glutaric acid_2TMS +293.12958 CC BY-NC 1508.447 Price et al., RECETOX, Masaryk University (CZ) Methionine_2TMS +340.14175 CC BY-NC 2274.972 Price et al., RECETOX, Masaryk University (CZ) Cysteine_4TMS +335.18893 CC BY-NC 1542.761 Price et al., RECETOX, Masaryk University (CZ) Cysteine_3TMS +305.15805 CC BY-NC 1420.506 Price et al., RECETOX, Masaryk University (CZ) beta-Alanine_3TMS +263.10043 CC BY-NC 1674.306 Price et al., RECETOX, Masaryk University (CZ) Acetylmethionine_1TMS +335.06458 CC BY-NC 1653.322 Price et al., RECETOX, Masaryk University (CZ) Acetylmethionine_2TMS +434.26306 CC BY-NC 1908.314 Price et al., RECETOX, Masaryk University (CZ) Lysine_4TMS +362.22369 CC BY-NC 1687.725 Price et al., RECETOX, Masaryk University (CZ) Lysine_3TMS +381.16385 CC BY-NC 1764.405 Price et al., RECETOX, Masaryk University (CZ) Methionine sulfoxide_3TMS +261.10855 CC BY-NC 1226.034 Price et al., RECETOX, Masaryk University (CZ) Valine_2TMS +390.15857 CC BY-NC 1883.896 Price et al., RECETOX, Masaryk University (CZ) Glucuro-3,6-lactone_3TMS isomer 1 +388.14252 CC BY-NC 1922.836 Price et al., RECETOX, Masaryk University (CZ) Glucuro-3,6-lactone_3TMS isomer 2 +451.21841 CC BY-NC 2614.971 Price et al., RECETOX, Masaryk University (CZ) Sucrose_8TMS +267.11365 CC BY-NC 1337.622 Price et al., RECETOX, Masaryk University (CZ) Itaconic acid_2TMS +462.20978 CC BY-NC 1782.877 Price et al., RECETOX, Masaryk University (CZ) Shikimic acid_4TMS +469.23215 CC BY-NC 1948.663 Price et al., RECETOX, Masaryk University (CZ) Epinepherine_4TMS +305.16257 CC BY-NC 1883.718 Price et al., RECETOX, Masaryk University (CZ) Tryptophol_2TMS +232.11545 CC BY-NC 1821.623 Price et al., RECETOX, Masaryk University (CZ) Tryptophol_1TMS +383.16971 CC BY-NC 1925.553 Price et al., RECETOX, Masaryk University (CZ) Tyrosine_3TMS +419.12936 CC BY-NC 2058.391 Price et al., RECETOX, Masaryk University (CZ) 3-Chlorotyrosine_3TMS +229.11282 CC BY-NC 1522.196 Price et al., RECETOX, Masaryk University (CZ) Acetylproline_1TMS +312.1207 CC BY-NC 1746.645 Price et al., RECETOX, Masaryk University (CZ) Vanillic acid_2TMS +335.17609 CC BY-NC 1438.379 Price et al., RECETOX, Masaryk University (CZ) Homoserine_3TMS +404.14093 CC BY-NC 1658.598 Price et al., RECETOX, Masaryk University (CZ) Homoserine_4TMS +384.16022 CC BY-NC 1813.416 Price et al., RECETOX, Masaryk University (CZ) Homogentisic acid_3TMS +418.99484 CC BY-NC 2505.27 Price et al., RECETOX, Masaryk University (CZ) Homocysteine_4TMS +351.15323 CC BY-NC 1645.979 Price et al., RECETOX, Masaryk University (CZ) Homocysteine_3TMS +464.18985 CC BY-NC 1932.408 Price et al., RECETOX, Masaryk University (CZ) Ascorbic acid_4TMS +498.86856 CC BY-NC 2728.015 Price et al., RECETOX, Masaryk University (CZ) Spermine_6TMS +578.1349 CC BY-NC 2238.332 Price et al., RECETOX, Masaryk University (CZ) Spermine_derivative +484.40952 CC BY-NC 3280.406 Price et al., RECETOX, Masaryk University (CZ) Stigmasterol_1TMS +194.07974 CC BY-NC 1843.997 Price et al., RECETOX, Masaryk University (CZ) Caffeine +509.22403 CC BY-NC 2077.476 Price et al., RECETOX, Masaryk University (CZ) Myo-inositol_6TMS +176.09434 CC BY-NC 1704.209 Price et al., RECETOX, Masaryk University (CZ) Cotinine +372.27695 CC BY-NC 2940.707 Price et al., RECETOX, Masaryk University (CZ) Progesterone +266.10165 CC BY-NC 1791.219 Price et al., RECETOX, Masaryk University (CZ) Acetylphenylalanine_1TMS +351.16812 CC BY-NC 1773.636 Price et al., RECETOX, Masaryk University (CZ) Acetylalanine_2TMS +456.18604 CC BY-NC 2079.217 Price et al., RECETOX, Masaryk University (CZ) Uric acid_4TMS +261.0784 CC BY-NC 1344.988 Price et al., RECETOX, Masaryk University (CZ) Citraconic acid_2TMS +314.08749 CC BY-NC 1708.782 Price et al., RECETOX, Masaryk University (CZ) Quinolinic aicd_2TMS +405.18152 CC BY-NC 1736.717 Price et al., RECETOX, Masaryk University (CZ) Acetylglutamic acid_3TMS +320.11572 CC BY-NC 1759.747 Price et al., RECETOX, Masaryk University (CZ) Acetylglutamic acid_2TMS +464.252 CC BY-NC 2446.155 Price et al., RECETOX, Masaryk University (CZ) Serotonin_4TMS +390.19714 CC BY-NC 2474.028 Price et al., RECETOX, Masaryk University (CZ) Serotonin_3TMS +368.15134 CC BY-NC 1998.854 Price et al., RECETOX, Masaryk University (CZ) Xanthine_3TMS +308.13397 CC BY-NC 1353.518 Price et al., RECETOX, Masaryk University (CZ) Serine_3TMS +380.17392 CC BY-NC 1559.921 Price et al., RECETOX, Masaryk University (CZ) Serine_4TMS +462.21869 CC BY-NC 2362.292 Price et al., RECETOX, Masaryk University (CZ) Acetyltryptophan_3TMS +390.17914 CC BY-NC 2417.979 Price et al., RECETOX, Masaryk University (CZ) Acetyltryptophan_2TMS isomer 1 +503.2298 CC BY-NC 2479.712 Price et al., RECETOX, Masaryk University (CZ) Tryptophan_derivative +386.14746 CC BY-NC 2531.8 Price et al., RECETOX, Masaryk University (CZ) Acetyltryptophan_2TMS isomer 2 +304.17181 CC BY-NC 1950.659 Price et al., RECETOX, Masaryk University (CZ) Tryptamine_2TMS +475.0034 CC BY-NC 2137.466 Price et al., RECETOX, Masaryk University (CZ) Tryptamine_derivative +359.02829 CC BY-NC 2197.85 Price et al., RECETOX, Masaryk University (CZ) Tryptamine_3TMS +374.20206 CC BY-NC 2210.789 Price et al., RECETOX, Masaryk University (CZ) Tryptamine_3TMS +416.25623 CC BY-NC 2684.039 Price et al., RECETOX, Masaryk University (CZ) Estradiol_2TMS +414.24042 CC BY-NC 2717.327 Price et al., RECETOX, Masaryk University (CZ) Dehydroestradiol_2TMS +426.20065 CC BY-NC 2174.229 Price et al., RECETOX, Masaryk University (CZ) Kynurenine_3TMS +484.6163 CC BY-NC 2127.988 Price et al., RECETOX, Masaryk University (CZ) Kynurenine_4TMS +363.17108 CC BY-NC 1603.813 Price et al., RECETOX, Masaryk University (CZ) Glutamic acid_3TMS spectra 1 +328.2792 CC BY-NC 2031.754 Price et al., RECETOX, Masaryk University (CZ) Palmitic acid_1TMS +350.14514 CC BY-NC 2149.28 Price et al., RECETOX, Masaryk University (CZ) Kynurenine_2TMS +341.01743 CC BY-NC 2140.445 Price et al., RECETOX, Masaryk University (CZ) 1-Octadecanol_1TMS +440.22937 CC BY-NC 2063.897 Price et al., RECETOX, Masaryk University (CZ) Dopamine_4TMS +369.12262 CC BY-NC 1803.491 Price et al., RECETOX, Masaryk University (CZ) Dopamine_3TMS +371.22736 CC BY-NC 2690.648 Price et al., RECETOX, Masaryk University (CZ) Estrone_1TMS +342.20087 CC BY-NC 2649.305 Price et al., RECETOX, Masaryk University (CZ) Estrone_1TMS +407.17627 CC BY-NC 2196.115 Price et al., RECETOX, Masaryk University (CZ) 5-Hydroxyindole-3-acetic acid_3TMS +519.20136 CC BY-NC 2427.129 Price et al., RECETOX, Masaryk University (CZ) Uridine_4TMS isomer 1 +517.20398 CC BY-NC 2478.395 Price et al., RECETOX, Masaryk University (CZ) Uridine_4TMS isomer 2 +326.26367 CC BY-NC 2012.293 Price et al., RECETOX, Masaryk University (CZ) Palmitoleic acid_1TMS +246.13393 CC BY-NC 1244.507 Price et al., RECETOX, Masaryk University (CZ) Norvaline_2TMS +323.03726 CC BY-NC 1469.973 Price et al., RECETOX, Masaryk University (CZ) Norvaline_3TMS +261.11807 CC BY-NC 1887.648 Price et al., RECETOX, Masaryk University (CZ) Methyl-3-indolylacetate_1TMS +486.42563 CC BY-NC 3342.255 Price et al., RECETOX, Masaryk University (CZ) beta-Sitosterol_1TMS +294.134 CC BY-NC 1622.569 Price et al., RECETOX, Masaryk University (CZ) Phenylalanine_2TMS +460.95105 CC BY-NC 1907.744 Price et al., RECETOX, Masaryk University (CZ) Homocitrulline_4TMS +278.10501 CC BY-NC 1497.347 Price et al., RECETOX, Masaryk University (CZ) Acetylserine_2TMS +456.37824 CC BY-NC 3220.533 Price et al., RECETOX, Masaryk University (CZ) 7-Dehydrocholesterol_1TMS +271.08026 CC BY-NC 1506.984 Price et al., RECETOX, Masaryk University (CZ) Salicylic acid_2TMS +557.59625 CC BY-NC 2684.795 Price et al., RECETOX, Masaryk University (CZ) Cytidine_5TMS +359.2977 CC BY-NC 2235.718 Price et al., RECETOX, Masaryk University (CZ) Stearic acid_1TMS +279.13321 CC BY-NC 1866.714 Price et al., RECETOX, Masaryk University (CZ) Adenine_2TMS +466.22934 CC BY-NC 1884.504 Price et al., RECETOX, Masaryk University (CZ) Galactose_5TMS isomer 1 +351.17252 CC BY-NC 1925.431 Price et al., RECETOX, Masaryk University (CZ) Adenine_3TMS +480.24384 CC BY-NC 1907.299 Price et al., RECETOX, Masaryk University (CZ) Galactose_5TMS isomer 2 +323.13168 CC BY-NC 1799.822 Price et al., RECETOX, Masaryk University (CZ) Hippuric acid_2TMS +238.07059 CC BY-NC 1842.755 Price et al., RECETOX, Masaryk University (CZ) Hippuric acid_1TMS +458.97305 CC BY-NC 1783.803 Price et al., RECETOX, Masaryk University (CZ) 2-Deoxyglucose_4TMS +359.11441 CC BY-NC 1734.565 Price et al., RECETOX, Masaryk University (CZ) 2,3-Dihydroxybenzoic acid_3TMS +468.37845 CC BY-NC 3053.203 Price et al., RECETOX, Masaryk University (CZ) Ergocalciferol_TMS +270.25577 CC BY-NC 1925.397 Price et al., RECETOX, Masaryk University (CZ) Methyl palmitate +259.07892 CC BY-NC 1551.845 Price et al., RECETOX, Masaryk University (CZ) Maleamic acid_2TMS isomer 2 +256.1189 CC BY-NC 1432.859 Price et al., RECETOX, Masaryk University (CZ) Maleamic acid_2TMS isomer 1 +331.14514 CC BY-NC 1526.203 Price et al., RECETOX, Masaryk University (CZ) Maleamic acid_3TMS +466.22998 CC BY-NC 1890.842 Price et al., RECETOX, Masaryk University (CZ) Glucose_5TMS isomer 1 +448.21909 CC BY-NC 1911.034 Price et al., RECETOX, Masaryk University (CZ) Glucose_5TMS isomer 2 +349.15625 CC BY-NC 1510.38 Price et al., RECETOX, Masaryk University (CZ) Aspartic acid_3TMS isomer +502.42047 CC BY-NC 3147.115 Price et al., RECETOX, Masaryk University (CZ) alpha-Tocopherol_1TMS +502.332 CC BY-NC 2250.516 Price et al., RECETOX, Masaryk University (CZ) Spermidine_5TMS +423.76837 CC BY-NC 2199.144 Price et al., RECETOX, Masaryk University (CZ) Spermidine_4TMS +255.11404 CC BY-NC 1517.806 Price et al., RECETOX, Masaryk University (CZ) Cytosine_2TMS +327.16107 CC BY-NC 1621.093 Price et al., RECETOX, Masaryk University (CZ) Cytosine_3TMS +462.2586 CC BY-NC 1850.448 Price et al., RECETOX, Masaryk University (CZ) Glycylvaline_4TMS +280.11725 CC BY-NC 1802.407 Price et al., RECETOX, Masaryk University (CZ) Hypoxanthine_2TMS +417.30649 CC BY-NC 2851.973 Price et al., RECETOX, Masaryk University (CZ) Pregnenolone_1TMS +471.2048 CC BY-NC 2088.587 Price et al., RECETOX, Masaryk University (CZ) Levodopa_4TMS +224.08672 CC BY-NC 1457.841 Price et al., RECETOX, Masaryk University (CZ) 2-Methoxybenzoic acid_1TMS +531.23712 CC BY-NC 2673.374 Price et al., RECETOX, Masaryk University (CZ) 5-Methylcytidine_4TMS isomer 1 +557.9187 CC BY-NC 2717.599 Price et al., RECETOX, Masaryk University (CZ) 5-Methylcytidine_4TMS isomer 2 +306.09992 CC BY-NC 1644.168 Price et al., RECETOX, Masaryk University (CZ) Acetylaspartic acid_2TMS +322.14883 CC BY-NC 1381.929 Price et al., RECETOX, Masaryk University (CZ) Threonine_3TMS spectra 1 +326.96603 CC BY-NC 1646.616 Price et al., RECETOX, Masaryk University (CZ) 2-Oxoadipic acid_2TMS isomer 2 +328.98157 CC BY-NC 1621.799 Price et al., RECETOX, Masaryk University (CZ) 2-Oxoadipic acid_2TMS isomer 1 +517.22162 CC BY-NC 2681.155 Price et al., RECETOX, Masaryk University (CZ) Cytidine_4TMS +456.37826 CC BY-NC 3260.078 Price et al., RECETOX, Masaryk University (CZ) Dehydrocholesterol_1TMS +466.36206 CC BY-NC 3289.183 Price et al., RECETOX, Masaryk University (CZ) Dehydroergosterol_1TMS +454.36246 CC BY-NC 3242.543 Price et al., RECETOX, Masaryk University (CZ) Cholestatrienol_1TMS +258.09448 CC BY-NC 1304.064 Price et al., RECETOX, Masaryk University (CZ) Proline_2TMS diff --git a/tools/scipy/test-data/reference.txt b/tools/analysis/test-data/reference.txt similarity index 100% rename from tools/scipy/test-data/reference.txt rename to tools/analysis/test-data/reference.txt diff --git a/tools/scipy/utils.py b/tools/analysis/utils.py similarity index 100% rename from tools/scipy/utils.py rename to tools/analysis/utils.py diff --git a/tools/scipy/.shed.yml b/tools/scipy/.shed.yml deleted file mode 100644 index 313737d9..00000000 --- a/tools/scipy/.shed.yml +++ /dev/null @@ -1,16 +0,0 @@ -name: scipy -owner: recetox -remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/scipy" -homepage_url: "https://docs.scipy.org/doc/scipy/tutorial/interpolate.html" -categories: - - Metabolomics - - Statistics -description: "Searching, filtering and converting mass spectral libraries." -long_description: "Tools to filter (normalize intensities, filter mz range, convert adducts, ...) and convert (msp/mgf/json) mass spectral libraries and to perform spectral, fingerprint and metadata similarity calculations as well as molecular networking." -auto_tool_repositories: - name_template: "{{ tool_id }}" - description_template: "{{ tool_name }} tool from the scipy package" -suite: - name: suite_scipy - description: tools from the scipy suite are used for science - type: repository_suite_definition \ No newline at end of file From 56c59c37eb2d3ec8da5af2f82fe698794149f5f7 Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 14 Nov 2024 16:29:01 +0100 Subject: [PATCH 4/9] updated gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 6d512d53..fed13a16 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ .vscode **/tool_test_output.html **/tool_test_output.json +**/tmp* +**/__pycache__ \ No newline at end of file From 9d57959f0e2083f621f9084b996c14f49e67906a Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 14 Nov 2024 16:29:07 +0100 Subject: [PATCH 5/9] added test data --- .../analysis/analysis_pandas_arithmetics.xml | 2 +- .../analysis_pandas_rename_column.xml | 0 tools/analysis/analysis_scipy_interpolate.xml | 2 +- .../arithmetics/query_divide_ri.tabular | 266 ++++++++++++++++++ .../interpolate/query_interpolate_rt.tabular | 266 ++++++++++++++++++ 5 files changed, 534 insertions(+), 2 deletions(-) create mode 100644 tools/analysis/analysis_pandas_rename_column.xml create mode 100644 tools/analysis/test-data/arithmetics/query_divide_ri.tabular create mode 100644 tools/analysis/test-data/interpolate/query_interpolate_rt.tabular diff --git a/tools/analysis/analysis_pandas_arithmetics.xml b/tools/analysis/analysis_pandas_arithmetics.xml index 544c85d3..a7ce9857 100644 --- a/tools/analysis/analysis_pandas_arithmetics.xml +++ b/tools/analysis/analysis_pandas_arithmetics.xml @@ -9,7 +9,7 @@ pyarrow pyarrow Date: Thu, 14 Nov 2024 16:54:39 +0100 Subject: [PATCH 6/9] another rename and adding the column rename tool --- .../analysis_pandas_rename_column.xml | 0 tools/{analysis => tables}/.shed.yml | 4 +- .../table_pandas_arithmetics.py} | 0 .../table_pandas_arithmetics.xml} | 2 +- tools/tables/table_pandas_rename_column.py | 30 ++++++++ tools/tables/table_pandas_rename_column.xml | 74 +++++++++++++++++++ .../table_scipy_interpolate.py} | 0 .../table_scipy_interpolate.xml} | 2 +- .../arithmetics/query_divide_ri.tabular | 0 .../interpolate/query_interpolate_rt.tabular | 0 .../test-data/query.tabular | 0 .../test-data/reference.txt | 0 tools/{analysis => tables}/utils.py | 0 13 files changed, 108 insertions(+), 4 deletions(-) delete mode 100644 tools/analysis/analysis_pandas_rename_column.xml rename tools/{analysis => tables}/.shed.yml (95%) rename tools/{analysis/analysis_pandas_arithmetics.py => tables/table_pandas_arithmetics.py} (100%) rename tools/{analysis/analysis_pandas_arithmetics.xml => tables/table_pandas_arithmetics.xml} (96%) create mode 100644 tools/tables/table_pandas_rename_column.py create mode 100644 tools/tables/table_pandas_rename_column.xml rename tools/{analysis/analysis_scipy_interpolate.py => tables/table_scipy_interpolate.py} (100%) rename tools/{analysis/analysis_scipy_interpolate.xml => tables/table_scipy_interpolate.xml} (98%) rename tools/{analysis => tables}/test-data/arithmetics/query_divide_ri.tabular (100%) rename tools/{analysis => tables}/test-data/interpolate/query_interpolate_rt.tabular (100%) rename tools/{analysis => tables}/test-data/query.tabular (100%) rename tools/{analysis => tables}/test-data/reference.txt (100%) rename tools/{analysis => tables}/utils.py (100%) diff --git a/tools/analysis/analysis_pandas_rename_column.xml b/tools/analysis/analysis_pandas_rename_column.xml deleted file mode 100644 index e69de29b..00000000 diff --git a/tools/analysis/.shed.yml b/tools/tables/.shed.yml similarity index 95% rename from tools/analysis/.shed.yml rename to tools/tables/.shed.yml index 4a0e1f89..19cbd631 100644 --- a/tools/analysis/.shed.yml +++ b/tools/tables/.shed.yml @@ -1,4 +1,4 @@ -name: analysis +name: tables owner: recetox remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/analysis" homepage_url: "https://github.com/RECETOX/galaxytools" @@ -11,6 +11,6 @@ auto_tool_repositories: name_template: "{{ tool_id }}" description_template: "{{ tool_name }} tool from the general purpose data analysis suite developed by RECETOX." suite: - name: suite_analysis + name: suite_table_tools description: This tool suites contains tools for general purpose data analysis built on top of pandas, scipy, dplyr and others. type: repository_suite_definition \ No newline at end of file diff --git a/tools/analysis/analysis_pandas_arithmetics.py b/tools/tables/table_pandas_arithmetics.py similarity index 100% rename from tools/analysis/analysis_pandas_arithmetics.py rename to tools/tables/table_pandas_arithmetics.py diff --git a/tools/analysis/analysis_pandas_arithmetics.xml b/tools/tables/table_pandas_arithmetics.xml similarity index 96% rename from tools/analysis/analysis_pandas_arithmetics.xml rename to tools/tables/table_pandas_arithmetics.xml index a7ce9857..40549a14 100644 --- a/tools/analysis/analysis_pandas_arithmetics.xml +++ b/tools/tables/table_pandas_arithmetics.xml @@ -9,7 +9,7 @@ pyarrow + of a table + + + 2.2.3 + 0 + + + + + + pandas + + + + + + + + + + + + + [0-9a-zA-Z_]+ + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/tools/analysis/analysis_scipy_interpolate.py b/tools/tables/table_scipy_interpolate.py similarity index 100% rename from tools/analysis/analysis_scipy_interpolate.py rename to tools/tables/table_scipy_interpolate.py diff --git a/tools/analysis/analysis_scipy_interpolate.xml b/tools/tables/table_scipy_interpolate.xml similarity index 98% rename from tools/analysis/analysis_scipy_interpolate.xml rename to tools/tables/table_scipy_interpolate.xml index 5f289076..b07191b7 100644 --- a/tools/analysis/analysis_scipy_interpolate.xml +++ b/tools/tables/table_scipy_interpolate.xml @@ -21,7 +21,7 @@ pyarrow Date: Thu, 14 Nov 2024 17:18:17 +0100 Subject: [PATCH 7/9] added tools to rename columns and added tests for the arithmetics tool --- tools/tables/table_pandas_arithmetics.xml | 10 ++++- tools/tables/table_pandas_rename_column.xml | 39 ++++++++++--------- .../rename/reference_both_renamed.tabular | 29 ++++++++++++++ .../rename/reference_rt_renamed.tabular | 29 ++++++++++++++ 4 files changed, 87 insertions(+), 20 deletions(-) create mode 100644 tools/tables/test-data/rename/reference_both_renamed.tabular create mode 100644 tools/tables/test-data/rename/reference_rt_renamed.tabular diff --git a/tools/tables/table_pandas_arithmetics.xml b/tools/tables/table_pandas_arithmetics.xml index 40549a14..ebe87fc6 100644 --- a/tools/tables/table_pandas_arithmetics.xml +++ b/tools/tables/table_pandas_arithmetics.xml @@ -35,7 +35,15 @@ - + + + + + + + + + This tool performs arithmetic operations on a specified column of a dataframe. Supported operations are: multiply, subtract, divide, add, and power. diff --git a/tools/tables/table_pandas_rename_column.xml b/tools/tables/table_pandas_rename_column.xml index 6b075e1c..32714e06 100644 --- a/tools/tables/table_pandas_rename_column.xml +++ b/tools/tables/table_pandas_rename_column.xml @@ -47,28 +47,29 @@ - + + + + + + + + + + + + + + + + + + - + 10.5281/zenodo.3509134 \ No newline at end of file diff --git a/tools/tables/test-data/rename/reference_both_renamed.tabular b/tools/tables/test-data/rename/reference_both_renamed.tabular new file mode 100644 index 00000000..6132b8d8 --- /dev/null +++ b/tools/tables/test-data/rename/reference_both_renamed.tabular @@ -0,0 +1,29 @@ +retention_index retention_time +1300 2.9 +1400 3.2 +1500 3.6 +1600 4.1 +1700 4.5 +1800 4.9 +1900 5.3 +2000 5.7 +2100 6.0 +2200 6.3 +2300 6.6 +2400 6.9 +2500 7.2 +2600 7.4 +2700 7.6 +2800 7.8 +2900 8.1 +3000 8.3 +3100 8.5 +3200 8.8 +3300 9.2 +3400 9.5 +3500 9.9 +3600 10.4 +3700 11.0 +3800 11.7 +3900 12.0 +4000 12.5 diff --git a/tools/tables/test-data/rename/reference_rt_renamed.tabular b/tools/tables/test-data/rename/reference_rt_renamed.tabular new file mode 100644 index 00000000..25a301c1 --- /dev/null +++ b/tools/tables/test-data/rename/reference_rt_renamed.tabular @@ -0,0 +1,29 @@ +RI retention_time +1300 2.9 +1400 3.2 +1500 3.6 +1600 4.1 +1700 4.5 +1800 4.9 +1900 5.3 +2000 5.7 +2100 6.0 +2200 6.3 +2300 6.6 +2400 6.9 +2500 7.2 +2600 7.4 +2700 7.6 +2800 7.8 +2900 8.1 +3000 8.3 +3100 8.5 +3200 8.8 +3300 9.2 +3400 9.5 +3500 9.9 +3600 10.4 +3700 11.0 +3800 11.7 +3900 12.0 +4000 12.5 From 0db7a67f5a5178997216757b1a5116f0793c4dda Mon Sep 17 00:00:00 2001 From: hechth Date: Thu, 14 Nov 2024 17:25:54 +0100 Subject: [PATCH 8/9] added test for the interpolation tool --- tools/tables/table_scipy_interpolate.xml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/tools/tables/table_scipy_interpolate.xml b/tools/tables/table_scipy_interpolate.xml index b07191b7..bd9e7451 100644 --- a/tools/tables/table_scipy_interpolate.xml +++ b/tools/tables/table_scipy_interpolate.xml @@ -53,7 +53,14 @@ - + + + + + + + + Date: Thu, 14 Nov 2024 18:19:54 +0100 Subject: [PATCH 9/9] fixed interpolate documentation --- tools/tables/table_scipy_interpolate.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/tables/table_scipy_interpolate.xml b/tools/tables/table_scipy_interpolate.xml index bd9e7451..99d79ac8 100644 --- a/tools/tables/table_scipy_interpolate.xml +++ b/tools/tables/table_scipy_interpolate.xml @@ -63,22 +63,22 @@