Mercurial > repos > ufz > dose_response_analysis_tool

comparison dose_response.xml @ 1:8a1b524ed9d8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit dca5f947ae4c9697ac0cfce0b313170b541124e5
author ufz
date Tue, 08 Oct 2024 12:41:07 +0000
parents 082e9d22c38d
children c122403ac78a
comparison
equal deleted inserted replaced
0:082e9d22c38d 1:8a1b524ed9d8
1 <tool id="dr_curve" name="Dose Response Curve for Toxicological Risk Assessment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0"> 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> 2 <description>for Toxicological Risk Assessment</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.0_1</token> 4 <token name="@TOOL_VERSION@">3.0.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <creator> 7 <creator>
8 <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" 8 <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology"
9 url ="https://www.ufz.de/index.php?en=34241"/> 9 url ="https://www.ufz.de/index.php?en=34241"/>
10 </creator> 10 </creator>
13 <requirement type="package" version="4.3.3">r-base</requirement> 13 <requirement type="package" version="4.3.3">r-base</requirement>
14 <requirement type="package" version="3.5.1">r-ggplot2</requirement> 14 <requirement type="package" version="3.5.1">r-ggplot2</requirement>
15 </requirements> 15 </requirements>
16 <command detect_errors="aggressive"> 16 <command detect_errors="aggressive">
17 <![CDATA[ 17 <![CDATA[
18 Rscript $__tool_directory__/dose_response.R 18 Rscript '$__tool_directory__'/dose_response.R
19 '$input_csv' 19 '$input_csv'
20 '$concentration_column' 20 '$concentration_column'
21 '$response_column' 21 '$response_column'
22 '$plot_output' 22 '$plot_output'
23 '$ec_output' 23 '$ec_output'
24 ]]> 24 ]]>
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <param name="input_csv" type="data" format="tabular" label="Concentration - Response Tabular Input"/> 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"/> 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"/> 29 <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column" help="Name of the column for response values"/>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data name="plot_output" format="jpg" label="Dose Response Plot"/> 32 <data name="plot_output" format="jpg" label="Dose Response Plot"/>
33 <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: EC Values"/> 33 <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: EC Values"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
37 <param name="input_csv" value="test_summary.tsv"/> 37 <param name="input_csv" value="drc_input.tsv"/>
38 <param name="concentration_column" value="concentration"/> 38 <param name="concentration_column" value="1"/>
39 <param name="response_column" value="lethal"/> 39 <param name="response_column" value="2"/>
40 <output name="plot_output" value="result.jpeg" ftype="jpg"/> 40 <output name="plot_output" ftype="jpg">
41 <output name="ec_output" value="results_EC.csv" ftype="csv" /> 41 <assert_contents>
42 <has_image_width width="480"/>
43 <has_image_height height="480"/>
44 </assert_contents>
45 </output>
46 <output name="ec_output" value="drc_EC_output.tsv" ftype="tabular" />
42 </test> 47 </test>
43 </tests> 48 </tests>
44 <help><![CDATA[ 49 <help><![CDATA[
45 This tool performs dose-response analysis on the provided CSV file, 50 This tool performs dose-response analysis on the provided CSV file,
46 generates a dose-response plot, and calculates EC values (EC10, EC25, EC50). 51 generates a dose-response plot, and calculates EC values (EC10, EC25, EC50).
47 52
48 - `input_csv`: A CSV file containing the dose-response data. 53 - `input_csv`: A TSV file containing the dose-response data.
49 - `concentration_column`: The name of the column in the CSV file that contains the concentration values. 54 - `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 55 - `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. 56 - `plot_output`: A JPG image file of the dose-response plot.
52 - `ec_output`: A CSV file containing the calculated EC values. 57 - `ec_output`: A tabular file containing the calculated EC values.
53 ]]></help> 58 ]]></help>
54 <citations> 59 <citations>
55 <citation type="doi">10.1371/journal.pone.0146021</citation> 60 <citation type="doi">10.1371/journal.pone.0146021</citation>
56 </citations> 61 </citations>
57 </tool> 62 </tool>