Mercurial > repos > iuc > deseq2
changeset 45:702bdf59d6c8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 2bcb448af8311320be0a970be37aa8ea4eed66b9
| author | iuc |
|---|---|
| date | Fri, 19 Dec 2025 08:09:31 +0000 |
| parents | 1cb33de18af5 |
| children | |
| files | deseq2.R deseq2.xml macros.xml |
| diffstat | 3 files changed, 24 insertions(+), 13 deletions(-) [+] |
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--- a/deseq2.R Tue Dec 09 17:43:58 2025 +0000 +++ b/deseq2.R Fri Dec 19 08:09:31 2025 +0000 @@ -127,12 +127,19 @@ trim <- function(x) gsub("^\\s+|\\s+$", "", x) +# Helper function to decode base64-encoded JSON +decode_base64_json <- function(encoded_str) { + decoded_bytes <- base64enc::base64decode(encoded_str) + decoded_str <- rawToChar(decoded_bytes) + return(decoded_str) +} + # switch on if 'factors' was provided: library("rjson") if (!is.null(opt$sample_sheet_mode)) { # Sample sheet mode: build factor_list from sample sheet - filenames_to_labels <- fromJSON(opt$files_to_labels) + filenames_to_labels <- fromJSON(decode_base64_json(opt$files_to_labels)) # Read sample sheet sample_sheet <- read.table(opt$sample_sheet, sep = "\t", header = TRUE, stringsAsFactors = FALSE) @@ -341,9 +348,9 @@ } else { # Original mode: factors provided directly parser <- newJSONParser() - parser$addData(opt$factors) + parser$addData(decode_base64_json(opt$factors)) factor_list <- parser$getObject() - filenames_to_labels <- fromJSON(opt$files_to_labels) + filenames_to_labels <- fromJSON(decode_base64_json(opt$files_to_labels)) # For original mode, extract reference and target levels from the first factor # In original mode: ref=level1 (denominator), target=level2 (numerator) -> log2(level2/level1)
--- a/deseq2.xml Tue Dec 09 17:43:58 2025 +0000 +++ b/deseq2.xml Fri Dec 19 08:09:31 2025 +0000 @@ -38,6 +38,7 @@ #import json #import os +#import base64 Rscript '${__tool_directory__}/deseq2.R' --cores \${GALAXY_SLOTS:-1} -o '$deseq_out' @@ -90,13 +91,13 @@ #for $group in $level.groups.value: #for $file in $select_data.countsFile.get_datasets_for_group($group): $count_files.append(str($file)) - $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) + $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) #end for #end for #else: #for $file in $level.countsFile: $count_files.append(str($file)) - $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) + $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) #end for #end if $temp_factor.append( {str($level.factorLevel): $count_files} ) @@ -109,9 +110,9 @@ $header #if $select_data.how != 'sample_sheet_contrasts': - -f '#echo json.dumps(temp_factor_names)#' + -f '#echo base64.b64encode(json.dumps(temp_factor_names).encode()).decode()#' #end if - -l '#echo json.dumps(filename_to_element_identifiers)#' + -l '#echo base64.b64encode(json.dumps(filename_to_element_identifiers).encode()).decode()#' #if $advanced_options.esf_cond.esf: #if $advanced_options.esf_cond.esf == "user": -e $advanced_options.esf_cond.size_factor_input @@ -154,7 +155,7 @@ <option value="sample_sheet_contrasts">Select contrasts from sample sheet columns</option> </param> <when value="group_tags"> - <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> + <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" /> <expand macro="factor_repeat"> <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/> </expand> @@ -165,7 +166,7 @@ </expand> </when> <when value="sample_sheet_contrasts"> - <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/> + <param name="countsFile" type="data_collection" collection_type="list" format="tabular,tsv" label="Count file(s) collection" /> <param name="sample_sheet" type="data" format="tabular" label="Sample sheet file" help="A tabular file containing at least two columns: one with the element identifiers (matching those in the collection) and one or more columns with factor levels."/> <conditional name="design_formula_mode"> <param name="mode" type="select" label="Design formula specification"> @@ -174,8 +175,7 @@ </param> <when value="automatic"> <param name="factor" type="data_column" use_header_names="true" data_ref="sample_sheet" multiple="true" optional="false" label="Factor levels column(s)" help="Select one or more columns from the sample sheet to define factor levels for DESeq2 analysis. First selected factor is the primary factor"/> - <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/> - <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/> + <expand macro="reference_target_levels"/> </when> <when value="custom"> <param name="design_formula" type="text" label="Design formula" help="Specify the design formula using R formula syntax (e.g., '~ condition' or '~ batch + condition'). Column names must match those in the sample sheet. The last factor in the formula is used as the primary factor for contrasts."> @@ -192,8 +192,7 @@ </valid> </sanitizer> </param> - <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/> - <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/> + <expand macro="reference_target_levels"/> </when> </conditional> </when>
--- a/macros.xml Tue Dec 09 17:43:58 2025 +0000 +++ b/macros.xml Fri Dec 19 08:09:31 2025 +0000 @@ -18,6 +18,10 @@ </repeat> </repeat> </xml> + <xml name="reference_target_levels"> + <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/> + <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@DESEQ2_VERSION@">bioconductor-deseq2</requirement> @@ -30,6 +34,7 @@ <requirement type="package" version="3.1.3">r-gplots</requirement> <requirement type="package" version="1.0.12">r-pheatmap</requirement> <requirement type="package" version="0.2.21">r-rjson</requirement> + <requirement type="package" version="0.1_3">r-base64enc</requirement> </requirements> </xml> <token name="@TOOL_VERSION@">2.11.40.8</token>