Mercurial > repos > mbernt > baseline_toxicity_calculator
comparison qsar1.xml @ 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 |
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| date | Tue, 09 Apr 2024 07:51:18 +0000 |
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| -1:000000000000 | 0:ce46f2008024 |
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| 1 <tool id="tt_baseline" name="Baseline toxicity calculator" version="0.1.0+galaxy0"> | |
| 2 <description>Toxicity prediction tool</description> | |
| 3 <creator> | |
| 4 <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" url ="https://www.ufz.de/index.php?en=34241"/> | |
| 5 </creator> | |
| 6 <requirements> | |
| 7 <requirement type="package" version="2.2.1">pandas</requirement> | |
| 8 </requirements> | |
| 9 <command detect_errors="aggressive"><![CDATA[ | |
| 10 python '$__tool_directory__/qsar1.py' | |
| 11 --function '$function' | |
| 12 --csv_input '$csv_input' | |
| 13 #if $function == "apply_linear_functions" | |
| 14 --functions_csv '$function_csv' | |
| 15 #end if | |
| 16 --output '$output' | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <conditional name="function_cond"> | |
| 20 <param name="function" type="select" label="Process to execute" help="Select pre-set QSAR models or personal linear functions"> | |
| 21 <option value="calculate_baseline">Pre-defined QSARs</option> | |
| 22 <option value="apply_linear_functions">Personal Linear Functions</option> | |
| 23 </param> | |
| 24 <when value="calculate_baseline"> | |
| 25 </when> | |
| 26 <when value="apply_linear_functions"> | |
| 27 <param name="function_csv" type="data" label="Personal linear functions input" format="tabular" help="Input your logD data as tabular file"/> | |
| 28 </when> | |
| 29 </conditional> | |
| 30 <param name="csv_input" type="data" label="logD data input" format="tabular" help="Input your logD data as tabular file"/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="output" format="tabular"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="function" value="calculate_baseline"/> | |
| 38 <param name="csv_input" value="qsar.tabular"/> | |
| 39 <output name="output" value="qsar_result.tsv" ftype="tabular"/> | |
| 40 </test> | |
| 41 <test> | |
| 42 <param name="function" value="apply_linear_functions"/> | |
| 43 <param name="csv_input" value="qsar.tabular"/> | |
| 44 <param name="function_csv" value="functions.tabular"/> | |
| 45 <output name="output" value="qsar_result_2.tsv" ftype="tabular"/> | |
| 46 </test> | |
| 47 </tests> | |
| 48 <help> | |
| 49 Features: | |
| 50 *calculate_baseline* | |
| 51 *** Estimate the EC50 for four different species. EC50 are expressed in mol/L *** | |
| 52 + Danio rerio log(1/EC50)= 0.99 * logDlipw + 0.78 | |
| 53 + Caenorhabditis elegans log(1/EC50)= 0.81 * logDlipw + 1.15 | |
| 54 + Daphnia magna log(1/EC50)= 0.82 * logDlipw + 1.48 | |
| 55 + 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) | |
| 56 *apply_linear_functions* | |
| 57 *** Estimate the EC50 or based on user input linear functions (assuming the format 'ax+b' or 'ax-b') *** | |
| 58 | |
| 59 Input format: Tabular file with column header and integers values for rows | |
| 60 Functions input: Tabular file with one column header and linear function in the format 'ax+b' or 'ax-b' for rows | |
| 61 </help> | |
| 62 <citations> | |
| 63 <citation type="doi">10.1021/acs.est.2c05217</citation> | |
| 64 <citation type="doi">10.1016/j.aquatox.2018.12.003</citation> | |
| 65 <citation type="doi">10.1016/S0048-9697(98)00157-0</citation> | |
| 66 </citations> | |
| 67 </tool> |