Mercurial > repos > ufz > dose_response_analysis_tool

comparison dose_response.xml @ 0:082e9d22c38d draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 3aebdcc7c5b266a30262402934ffaad2a58adbcb
author ufz
date Mon, 10 Jun 2024 11:57:52 +0000
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-1:000000000000 0:082e9d22c38d
1 <tool id="dr_curve" name="Dose Response Curve for Toxicological Risk Assessment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>Toxicity prediction tool - Dose response Curve</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.0_1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <creator>
8 <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology"
9 url ="https://www.ufz.de/index.php?en=34241"/>
10 </creator>
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">r-drc</requirement>
13 <requirement type="package" version="4.3.3">r-base</requirement>
14 <requirement type="package" version="3.5.1">r-ggplot2</requirement>
15 </requirements>
16 <command detect_errors="aggressive">
17 <![CDATA[
18 Rscript $__tool_directory__/dose_response.R
19 '$input_csv'
20 '$concentration_column'
21 '$response_column'
22 '$plot_output'
23 '$ec_output'
24 ]]>
25 </command>
26 <inputs>
27 <param name="input_csv" type="data" format="tabular" label="Concentration - Response Tabular Input"/>
28 <param name="concentration_column" type="data_column" data_ref="input_csv" label="Concentration Column" help="Name of the column for concentration values"/>
29 <param name="response_column" type="data_column" label="Response Column" help="Name of the column for response values"/>
30 </inputs>
31 <outputs>
32 <data name="plot_output" format="jpg" label="Dose Response Plot"/>
33 <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: EC Values"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="input_csv" value="test_summary.tsv"/>
38 <param name="concentration_column" value="concentration"/>
39 <param name="response_column" value="lethal"/>
40 <output name="plot_output" value="result.jpeg" ftype="jpg"/>
41 <output name="ec_output" value="results_EC.csv" ftype="csv" />
42 </test>
43 </tests>
44 <help><![CDATA[
45 This tool performs dose-response analysis on the provided CSV file,
46 generates a dose-response plot, and calculates EC values (EC10, EC25, EC50).
47
48 - `input_csv`: A CSV file containing the dose-response data.
49 - `concentration_column`: The name of the column in the CSV file that contains the concentration values.
50 - `response_column`: The name of the column in the CSV file that contains the response values
51 - `plot_output`: A JPG image file of the dose-response plot.
52 - `ec_output`: A CSV file containing the calculated EC values.
53 ]]></help>
54 <citations>
55 <citation type="doi">10.1371/journal.pone.0146021</citation>
56 </citations>
57 </tool>