Mercurial > repos > mbernt > baseline_toxicity_calculator
changeset 0:ce46f2008024 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
| author | mbernt |
|---|---|
| date | Tue, 09 Apr 2024 07:51:18 +0000 |
| parents | |
| children | |
| files | qsar1.py qsar1.xml test-data/functions.tabular test-data/qsar.tabular test-data/qsar_result.tsv test-data/qsar_result_2.tsv test-data/result.tsv test-data/table.tsv |
| diffstat | 8 files changed, 129 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qsar1.py Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,39 @@ +import argparse +import re + +import pandas as pd + +parser = argparse.ArgumentParser(description='Calculate baseline toxicity for different aquatic species') +parser.add_argument('--function', type=str, choices=['calculate_baseline', 'apply_linear_functions'], + help='Function to execute') +parser.add_argument('--csv_input', type=argparse.FileType('r'), help='Path to the input csv file') +parser.add_argument('--functions_csv', type=argparse.FileType('r'), default=None, + help='Path to the csv file containing functions (only for apply_linear_functions)') +parser.add_argument('--output', type=argparse.FileType('w'), help='Path for the output csv file') +args = parser.parse_args() + +if args.function == 'calculate_baseline': + df = pd.read_csv(args.csv_input) + df.iloc[:, 0] = df.iloc[:, 0].astype(int) + df['Caenorhabditis elegans [mol/L]'] = 10 ** (-(0.81 * df.iloc[:, 0] + 1.15)) + df['Daphia magna [mol/L]'] = 10 ** (-(0.82 * df.iloc[:, 0] + 1.48)) + df['Danio rerio [mol/L]'] = 10 ** (-(0.99 * df.iloc[:, 0] + 0.78)) + df['Generic Human Cells [mol/L]'] = 0.026 / (10 ** df.iloc[:, 0]) * (1 + 10 ** (0.7 * df.iloc[:, 0] + 0.34) * 3 * 0.001 + 10 ** 3 * 0.07 * 0.001) + df.to_csv(args.output, index=False) + +elif args.function == 'apply_linear_functions': + df = pd.read_csv(args.csv_input) + functions_df = pd.read_csv(args.functions_csv) + + def parse_and_apply_equation(equation, x_values): + # Extract 'a' and 'b' from the equation (assuming the format 'ax+b' or 'ax-b') + pattern = re.compile(r'([+-]?\d*\.?\d*)x([+-]\d+)?') + match = pattern.search(equation) + a = float(match.group(1)) if match.group(1) not in ('', '+', '-') else 1.0 + b = float(match.group(2)) if match.group(2) else 0 + return a * x_values + b + + for i, row in functions_df.iterrows(): + func = row['function'] + df[f'result_{i}'] = parse_and_apply_equation(func, df['logD']) + df.to_csv(args.output, index=False)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qsar1.xml Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,67 @@ +<tool id="tt_baseline" name="Baseline toxicity calculator" version="0.1.0+galaxy0"> + <description>Toxicity prediction tool</description> + <creator> + <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" url ="https://www.ufz.de/index.php?en=34241"/> + </creator> + <requirements> + <requirement type="package" version="2.2.1">pandas</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/qsar1.py' + --function '$function' + --csv_input '$csv_input' + #if $function == "apply_linear_functions" + --functions_csv '$function_csv' + #end if + --output '$output' + ]]></command> + <inputs> + <conditional name="function_cond"> + <param name="function" type="select" label="Process to execute" help="Select pre-set QSAR models or personal linear functions"> + <option value="calculate_baseline">Pre-defined QSARs</option> + <option value="apply_linear_functions">Personal Linear Functions</option> + </param> + <when value="calculate_baseline"> + </when> + <when value="apply_linear_functions"> + <param name="function_csv" type="data" label="Personal linear functions input" format="tabular" help="Input your logD data as tabular file"/> + </when> + </conditional> + <param name="csv_input" type="data" label="logD data input" format="tabular" help="Input your logD data as tabular file"/> +</inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="function" value="calculate_baseline"/> + <param name="csv_input" value="qsar.tabular"/> + <output name="output" value="qsar_result.tsv" ftype="tabular"/> + </test> + <test> + <param name="function" value="apply_linear_functions"/> + <param name="csv_input" value="qsar.tabular"/> + <param name="function_csv" value="functions.tabular"/> + <output name="output" value="qsar_result_2.tsv" ftype="tabular"/> + </test> + </tests> + <help> + Features: + *calculate_baseline* + *** Estimate the EC50 for four different species. EC50 are expressed in mol/L *** + + Danio rerio log(1/EC50)= 0.99 * logDlipw + 0.78 + + Caenorhabditis elegans log(1/EC50)= 0.81 * logDlipw + 1.15 + + Daphnia magna log(1/EC50)= 0.82 * logDlipw + 1.48 + + Generic Human Cell log(1/EC50)= 0.026 / (10**logDlipw) * (1 + 10**(0.7*logDlipw+0.34) * 3 * 0.001 + 10**(3) * 0.07 * 0.001) + *apply_linear_functions* + *** Estimate the EC50 or based on user input linear functions (assuming the format 'ax+b' or 'ax-b') *** + + Input format: Tabular file with column header and integers values for rows + Functions input: Tabular file with one column header and linear function in the format 'ax+b' or 'ax-b' for rows + </help> + <citations> + <citation type="doi">10.1021/acs.est.2c05217</citation> + <citation type="doi">10.1016/j.aquatox.2018.12.003</citation> + <citation type="doi">10.1016/S0048-9697(98)00157-0</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/functions.tabular Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,4 @@ +function +2x+5 +1.87x-0.5 +2.36x+1.02 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qsar.tabular Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,5 @@ +logD +2 +1.36 +5 +3.6 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qsar_result.tsv Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,5 @@ +logD,Caenorhabditis elegans [mol/L],Daphia magna [mol/L],Danio rerio [mol/L],Generic Human Cells [mol/L] +2.0,0.0016982436524617442,0.0007585775750291835,0.0017378008287493763,0.00032106418816089466 +1.0,0.01096478196143185,0.005011872336272725,0.016982436524617443,0.0028675252992991685 +5.0,6.309573444801917e-06,2.6302679918953817e-06,1.8620871366628656e-06,5.674481573167704e-06 +3.0,0.00026302679918953814,0.0001148153621496883,0.00017782794100389227,4.9302983886037675e-05
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qsar_result_2.tsv Tue Apr 09 07:51:18 2024 +0000 @@ -0,0 +1,5 @@ +logD,result_0,result_1,result_2 +2.0,9.0,3.74,5.72 +1.36,7.720000000000001,2.5432,4.2096 +5.0,15.0,9.350000000000001,12.799999999999999 +3.6,12.2,6.732,9.496