diff dose_response.xml @ 0:082e9d22c38d draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tools/tox_tools/baseline_calculator commit 3aebdcc7c5b266a30262402934ffaad2a58adbcb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dose_response.xml	Mon Jun 10 11:57:52 2024 +0000
@@ -0,0 +1,57 @@
+<tool id="dr_curve" name="Dose Response Curve for Toxicological Risk Assessment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>Toxicity prediction tool - Dose response Curve</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.0_1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology"
+                      url ="https://www.ufz.de/index.php?en=34241"/>
+    </creator>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">r-drc</requirement>
+        <requirement type="package" version="4.3.3">r-base</requirement>
+        <requirement type="package" version="3.5.1">r-ggplot2</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        Rscript $__tool_directory__/dose_response.R
+            '$input_csv'
+            '$concentration_column'
+            '$response_column'
+            '$plot_output'
+            '$ec_output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_csv" type="data" format="tabular" label="Concentration - Response Tabular Input"/>
+        <param name="concentration_column" type="data_column" data_ref="input_csv" label="Concentration Column" help="Name of the column for concentration values"/>
+        <param name="response_column" type="data_column" label="Response Column" help="Name of the column for response values"/>
+    </inputs>
+    <outputs>
+        <data name="plot_output" format="jpg" label="Dose Response Plot"/>
+        <data name="ec_output" format="tabular" label="${tool.name} on ${on_string}: EC Values"/>
+    </outputs>
+        <tests>
+        <test>
+            <param name="input_csv" value="test_summary.tsv"/>
+            <param name="concentration_column" value="concentration"/>
+            <param name="response_column" value="lethal"/>
+            <output name="plot_output" value="result.jpeg" ftype="jpg"/>
+            <output name="ec_output" value="results_EC.csv" ftype="csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool performs dose-response analysis on the provided CSV file,
+        generates a dose-response plot, and calculates EC values (EC10, EC25, EC50).
+
+        - `input_csv`: A CSV file containing the dose-response data.
+        - `concentration_column`: The name of the column in the CSV file that contains the concentration values.
+        - `response_column`: The name of the column in the CSV file that contains the response values
+        - `plot_output`: A JPG image file of the dose-response plot.
+        - `ec_output`: A CSV file containing the calculated EC values.
+    ]]></help>
+        <citations>
+    <citation type="doi">10.1371/journal.pone.0146021</citation>
+    </citations>
+</tool>