From fcf6a4df15ca247a7b24082e29b6d42ab128e216 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 30 Oct 2024 12:07:02 +0100
Subject: [PATCH] Add missing quotes in decoupler bseudobulk tools

---
 .../decoupler/decoupler_pathway_inference.xml             | 8 ++++----
 .../tertiary-analysis/decoupler/decoupler_pseudobulk.xml  | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml
index 4fc2645a..a4c3b9df 100644
--- a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml
+++ b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml
@@ -1,4 +1,4 @@
-<tool id="decoupler_pathway_inference" name="Decoupler Pathway Inference" version="1.4.0+galaxy0" profile="20.05" license="MIT">
+<tool id="decoupler_pathway_inference" name="Decoupler Pathway Inference" version="1.4.0+galaxy1" profile="20.05" license="MIT">
     <description>
         of functional genesets/pathways for scRNA-seq data.
     </description>
@@ -12,9 +12,9 @@
             --min_n "$min_n"
             --method '$method'
             $use_raw
-            --source $source
-            --target $target
-            --weight $weight
+            --source '$source'
+            --target '$target'
+            --weight '$weight'
             --output "inference"
             $write_activities_path
     </command>
diff --git a/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml b/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml
index 171b6914..891fb526 100644
--- a/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml
+++ b/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml
@@ -1,4 +1,4 @@
-<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy7" profile="20.05">
+<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy8" profile="20.05">
     <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>
@@ -6,7 +6,7 @@
     <command detect_errors="exit_code"><![CDATA[
 mkdir deseq_output_dir &&
 mkdir plots_output_dir &&
-python '$__tool_directory__/decoupler_pseudobulk.py' $input_file
+python '$__tool_directory__/decoupler_pseudobulk.py' '$input_file'
     #if $adata_obs_fields_to_merge:
     --adata_obs_fields_to_merge '$adata_obs_fields_to_merge'
     #end if