Mercurial > repos > ufz > dose_response_analysis_tool
changeset 1:8a1b524ed9d8 draft
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 |
| files | dose_response.R dose_response.xml test-data/drc_EC_output.tsv test-data/drc_input.tsv test-data/test_summary.csv test-data/test_summary.tsv |
| diffstat | 6 files changed, 34 insertions(+), 29 deletions(-) [+] |
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--- a/dose_response.R Mon Jun 10 11:57:52 2024 +0000 +++ b/dose_response.R Tue Oct 08 12:41:07 2024 +0000 @@ -45,10 +45,14 @@ plot.background = element_rect(fill = "white", color = NA) ) - ggsave(filename = plot_file, plot = p, device = "jpg") + jpeg(filename = plot_file) + print(p) + dev.off() } dose_response_analysis <- function(data, concentration_col, response_col, plot_file, ec_file) { + concentration_col <- colnames(data)[as.integer(concentration_col)] + response_col <- colnames(data)[as.integer(response_col)] models <- fit_models(data, concentration_col, response_col) best_model_info <- select_best_model(models) ec_values <- calculate_ec_values(best_model_info$model) @@ -59,7 +63,7 @@ EC25 = ec_values$EC25[1], EC50 = ec_values$EC50[1] ) - write.csv(ec_data, ec_file, row.names = FALSE) + write.table(ec_data, ec_file, sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE) return(list(best_model = best_model_info$name, ec_values = ec_values)) } @@ -72,5 +76,5 @@ plot_file <- args[4] ec_file <- args[5] -data <- read.csv(data_file, header = TRUE) +data <- read.csv(data_file, header = TRUE, sep = "\t") dose_response_analysis(data, concentration_col, response_col, plot_file, ec_file)
--- a/dose_response.xml Mon Jun 10 11:57:52 2024 +0000 +++ b/dose_response.xml Tue Oct 08 12:41:07 2024 +0000 @@ -1,8 +1,8 @@ <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> + <description>for Toxicological Risk Assessment</description> <macros> - <token name="@TOOL_VERSION@">3.0_1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">3.0.1</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <creator> <organization name="Helmholtz Centre for Environmental Research - UFZ, Department of Ecotoxicology" @@ -15,7 +15,7 @@ </requirements> <command detect_errors="aggressive"> <![CDATA[ - Rscript $__tool_directory__/dose_response.R + Rscript '$__tool_directory__'/dose_response.R '$input_csv' '$concentration_column' '$response_column' @@ -26,7 +26,7 @@ <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"/> + <param name="response_column" type="data_column" data_ref="input_csv" label="Response Column" help="Name of the column for response values"/> </inputs> <outputs> <data name="plot_output" format="jpg" label="Dose Response Plot"/> @@ -34,22 +34,27 @@ </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" /> + <param name="input_csv" value="drc_input.tsv"/> + <param name="concentration_column" value="1"/> + <param name="response_column" value="2"/> + <output name="plot_output" ftype="jpg"> + <assert_contents> + <has_image_width width="480"/> + <has_image_height height="480"/> + </assert_contents> + </output> + <output name="ec_output" value="drc_EC_output.tsv" ftype="tabular" /> </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. + - `input_csv`: A TSV 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. + - `ec_output`: A tabular file containing the calculated EC values. ]]></help> <citations> <citation type="doi">10.1371/journal.pone.0146021</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/drc_EC_output.tsv Tue Oct 08 12:41:07 2024 +0000 @@ -0,0 +1,2 @@ +EC10 EC25 EC50 +5.08340659604631 10.6579575265526 22.3456566952853
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/drc_input.tsv Tue Oct 08 12:41:07 2024 +0000 @@ -0,0 +1,8 @@ +conc resp +0 0 +5 0.1 +10 0.3 +25 0.5 +50 0.6 +75 0.9 +100 1