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comparison dose_response.xml @ 3:2aa9da0a84a4 draft default tip

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/tox_tools/dose_responses commit 707eca86fc2de2e563fb5c89889f54eb13f529d0
author ufz
date Tue, 21 Jan 2025 12:26:00 +0000
parents c122403ac78a
children
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2:c122403ac78a 3:2aa9da0a84a4
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>for Toxicological Risk Assessment</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@">3</token> 5 <token name="@VERSION_SUFFIX@">4</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>
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 '$replicate_column'
22 '$plot_output' 23 '$plot_output'
23 '$ec_output' 24 '$ec_output'
24 '$compound_name' 25 '$compound_name'
25 '$concentration_unit' 26 '$concentration_unit'
26 ]]> 27 ]]>
27 </command> 28 </command>
28 <inputs> 29 <inputs>
29 <param name="input_csv" type="data" format="tabular" label="Dose-Response Tabular Input"/> 30 <param name="input_csv" type="data" format="tabular" label="Dose-Response Tabular Input"/>
30 <param name="concentration_column" type="data_column" data_ref="input_csv" label="Dose/Concentration Column Index" help="Index of the column for concentration values"/> 31 <param name="concentration_column" type="data_column" data_ref="input_csv" label="Dose/Concentration Column Index" help="Index of the column for concentration values"/>
31 <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column Index" help="Index of the column for response values"/> 32 <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column Index" help="Index of the column for response values"/>
33 <param name="replicate_column" type="data_column" data_ref="input_csv" label="Replicate Column Index" help="Index of the column for replicate values"/>
32 <param name="compound_name" type="text" label="Compound Name" help="Name of the compound to analyze"> 34 <param name="compound_name" type="text" label="Compound Name" help="Name of the compound to analyze">
33 <validator type="regex" message="Enter a valid compound name">^^[a-zA-Z0-9\[\]()_-]+$</validator> 35 <validator type="regex" message="Enter a valid compound name">^^[a-zA-Z0-9\[\]()_-]+$</validator>
34 </param> 36 </param>
35 <param name="concentration_unit" type="text" label="Concentration Unit (i.e. mg/L, µM)"> 37 <param name="concentration_unit" type="text" label="Concentration Unit (i.e. mg/L, µM)">
36 <validator type="regex" message="Enter a valid concentration unit">^(\S+/\S+)</validator> 38 <validator type="regex" message="Enter a valid concentration unit">^(\S+/\S+)</validator>
43 <tests> 45 <tests>
44 <test> 46 <test>
45 <param name="input_csv" value="drc_input.tsv"/> 47 <param name="input_csv" value="drc_input.tsv"/>
46 <param name="concentration_column" value="2"/> 48 <param name="concentration_column" value="2"/>
47 <param name="response_column" value="3"/> 49 <param name="response_column" value="3"/>
50 <param name="replicate_column" value="1"/>
48 <param name="compound_name" value="test-chemical"/> 51 <param name="compound_name" value="test-chemical"/>
49 <param name="concentration_unit" value="mg/L"/> 52 <param name="concentration_unit" value="mg/L"/>
50 <output name="plot_output" value="image_output.jpg" ftype="jpg"> 53 <output name="plot_output" value="image_output.jpg" ftype="jpg">
51 <assert_contents> 54 <assert_contents>
52 <has_image_width width="480"/> 55 <has_image_width width="480"/>
55 </output> 58 </output>
56 <output name="ec_output" value="drc_EC_output.tsv" ftype="tabular" /> 59 <output name="ec_output" value="drc_EC_output.tsv" ftype="tabular" />
57 </test> 60 </test>
58 </tests> 61 </tests>
59 <help><![CDATA[ 62 <help><![CDATA[
60 This tool performs dose-response analysis on the provided CSV file, 63 This tool performs dose-response analysis on the provided CSV/TSV file,
61 generates a dose-response plot, and calculates EC values (EC10, EC25, EC50). 64 generates a dose-response plot, and calculates three Effect Concentrations (EC) values (EC10, EC25, EC50).
65 The tool further calculate the AIC and the model summary.
62 66
63 - `input_csv`: A TSV file containing the dose-response data. 67 The tool need three inputs from the CSV/TSV file:
64 - `concentration_column`: The name of the column in the CSV file that contains the concentration values. 68 - One column with the replicate number
65 - `response_column`: The name of the column in the CSV file that contains the response values 69 - One column with concentrations values
66 - `plot_output`: A JPG image file of the dose-response plot. 70 - One column with biological response
67 - `ec_output`: A tabular file containing the calculated EC values. 71
72 An exemplary input might look like:
73
74 +------------+---------------+---------------+
75 | rep | conc | resp |
76 +============+===============+===============+
77 | 1 | 0 | 0 |
78 +------------+---------------+---------------+
79 | 2 | 10 | 50 |
80 +------------+---------------+---------------+
81 | 1 | 5 | 10 |
82 +------------+---------------+---------------+
83
84 **NOTE: Input Table must have column headers!**
85
86
68 ]]></help> 87 ]]></help>
69 <citations> 88 <citations>
70 <citation type="doi">10.1371/journal.pone.0146021</citation> 89 <citation type="doi">10.1371/journal.pone.0146021</citation>
71 </citations> 90 </citations>
72 </tool> 91 </tool>