Mercurial > repos > mbernt > baseline_toxicity_calculator

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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
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ce46f2008024 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 008f820fb9b8ec547e00205f809f982b8f4b8318
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1 <tool id="tt_baseline" name="Baseline toxicity calculator" version="0.1.0+galaxy0">
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2 <description>Toxicity prediction tool</description>
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3 <creator>
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4 <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" url ="https://www.ufz.de/index.php?en=34241"/>
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5 </creator>
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6 <requirements>
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7 <requirement type="package" version="2.2.1">pandas</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/qsar1.py'
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11 --function '$function'
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12 --csv_input '$csv_input'
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13 #if $function == "apply_linear_functions"
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14 --functions_csv '$function_csv'
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15 #end if
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16 --output '$output'
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17 ]]></command>
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18 <inputs>
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19 <conditional name="function_cond">
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20 <param name="function" type="select" label="Process to execute" help="Select pre-set QSAR models or personal linear functions">
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21 <option value="calculate_baseline">Pre-defined QSARs</option>
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22 <option value="apply_linear_functions">Personal Linear Functions</option>
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23 </param>
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24 <when value="calculate_baseline">
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25 </when>
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26 <when value="apply_linear_functions">
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27 <param name="function_csv" type="data" label="Personal linear functions input" format="tabular" help="Input your logD data as tabular file"/>
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28 </when>
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29 </conditional>
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30 <param name="csv_input" type="data" label="logD data input" format="tabular" help="Input your logD data as tabular file"/>
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31 </inputs>
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32 <outputs>
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33 <data name="output" format="tabular"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="function" value="calculate_baseline"/>
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38 <param name="csv_input" value="qsar.tabular"/>
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39 <output name="output" value="qsar_result.tsv" ftype="tabular"/>
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40 </test>
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41 <test>
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42 <param name="function" value="apply_linear_functions"/>
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43 <param name="csv_input" value="qsar.tabular"/>
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44 <param name="function_csv" value="functions.tabular"/>
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45 <output name="output" value="qsar_result_2.tsv" ftype="tabular"/>
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46 </test>
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47 </tests>
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48 <help>
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49 Features:
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50 *calculate_baseline*
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51 *** Estimate the EC50 for four different species. EC50 are expressed in mol/L ***
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52 + Danio rerio log(1/EC50)= 0.99 * logDlipw + 0.78
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53 + Caenorhabditis elegans log(1/EC50)= 0.81 * logDlipw + 1.15
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54 + Daphnia magna log(1/EC50)= 0.82 * logDlipw + 1.48
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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)
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56 *apply_linear_functions*
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57 *** Estimate the EC50 or based on user input linear functions (assuming the format 'ax+b' or 'ax-b') ***
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58
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59 Input format: Tabular file with column header and integers values for rows
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60 Functions input: Tabular file with one column header and linear function in the format 'ax+b' or 'ax-b' for rows
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1021/acs.est.2c05217</citation>
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64 <citation type="doi">10.1016/j.aquatox.2018.12.003</citation>
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65 <citation type="doi">10.1016/S0048-9697(98)00157-0</citation>
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66 </citations>
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67 </tool>