From 8d5a33b43d46175ad0177ddd23b5389554fe321c Mon Sep 17 00:00:00 2001
From: Tom Harrop <tharrop@unimelb.edu.au>
Date: Thu, 2 Nov 2023 20:36:41 +1100
Subject: [PATCH] quotes

---
 .../repeatexplorer2/repex_full_clustering.xml | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/tools/repeatexplorer2/repex_full_clustering.xml b/tools/repeatexplorer2/repex_full_clustering.xml
index 6922862..683612d 100644
--- a/tools/repeatexplorer2/repex_full_clustering.xml
+++ b/tools/repeatexplorer2/repex_full_clustering.xml
@@ -13,34 +13,34 @@
       &&
 
       ## output will go here
-      mkdir -p "${ReportFile.extra_files_path}"
+      mkdir -p '${ReportFile.extra_files_path}'
       &&
 
       /repex_tarean/seqclust
       --cpu \${GALAXY_SLOTS:-1}
       --max_memory \${GALAXY_MEMORY_KB}
-      "${paired}"
+      '${paired}'
       #if $sample:
-        --sample "${sample}"
+        --sample '${sample}'
       #end if
-      --taxon "${taxon}"
-      --output_dir="${ReportFile.extra_files_path}"
+      --taxon '${taxon}'
+      --output_dir='${ReportFile.extra_files_path}'
       #if $advanced.mincl:
-        --mincl "${advanced.mincl}"
+        --mincl '${advanced.mincl}'
       #end if
-      --assembly_min "${advanced.assembly_min}"
+      --assembly_min '${advanced.assembly_min}'
       #if $advanced.keep_names:
         --keep_names
       #end if
-      "${FastaFile}"
+      '${FastaFile}'
       &&
 
       ## archive the output
-      tar -cvf "${ReportArchive}" --directory="${ReportFile.extra_files_path}" .
+      tar -cvf '${ReportArchive}' --directory='${ReportFile.extra_files_path}' .
       &&
 
       ## pick up the html index
-      cp "${ReportFile.extra_files_path}/index.html" ./index.html
+      cp '${ReportFile.extra_files_path}/index.html' ./index.html
 
       ]]></command>
   <inputs>