From 5b0e66e4c73c7684b389035705b5d69c06d56be4 Mon Sep 17 00:00:00 2001
From: KristinaGomoryova <gomoryova@sci.muni.cz>
Date: Mon, 13 Jan 2025 09:42:48 +0100
Subject: [PATCH] save scp object as rds instead of RData

---
 tools/scp/macros.xml       | 2 +-
 tools/scp/scp_workflow.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/scp/macros.xml b/tools/scp/macros.xml
index 822a298c9..d56047064 100644
--- a/tools/scp/macros.xml
+++ b/tools/scp/macros.xml
@@ -232,7 +232,7 @@
 
         <section name="data_export" title="Export data" expanded="true">
             <param name="export_tables" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export intermediate results" help="Whether only the final result table (log2 transformed, normalized, imputed, batch-corrected data) should be exported or all intermediate results."/>
-            <param name="export_RData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export scp object as RData" help="Whether to export the scp object as RData."/>
+            <param name="export_RData" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export scp object as .rds" help="Whether to export the scp object as rds file format."/>
             <param name="export_R_script" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Export the R script to reproduce the analysis"
                 help="Check this box to export the script executed in the Galaxy tool as an R file to be able to reproduce the same processing offline. Not that in this case, the file paths need to be altered and all the dependencies have to be managed manually."/>
         </section>
diff --git a/tools/scp/scp_workflow.xml b/tools/scp/scp_workflow.xml
index 818b4fa95..204771f82 100644
--- a/tools/scp/scp_workflow.xml
+++ b/tools/scp/scp_workflow.xml
@@ -413,7 +413,7 @@
             <discover_datasets pattern="__name_and_ext__" directory="outputs" />
             <filter>data_export['export_tables']</filter>
         </collection>
-        <data name="scp_object" format="RData" label="scp object as RData">
+        <data name="scp_object" format="rds" label="scp object as .rds">
             <filter>data_export['export_RData']</filter>
         </data>
         <data name="script" format="txt" label="R script">