--- a/vsnp_build_tables.xml	Thu Jul 29 13:52:48 2021 +0000
+++ b/vsnp_build_tables.xml	Thu Jul 29 15:02:47 2021 +0000
@@ -22,17 +22,17 @@
     mkdir $input_json_dir &&
     #for $i in $input_type_cond.input_avg_mq_json_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_snps_json_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_json_dir/$identifier' &&
     #end for
     #for $i in $input_type_cond.input_newick_collection:
         #set file_name = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
         ln -s '$file_name' '$input_newick_dir/$identifier' &&
     #end for
 #end if
@@ -139,12 +139,12 @@
             </param>
             <param name="gbk_param" value="no"/>
             <output_collection name="excel" type="list" count="6">
-                <element name="Mbovis-01D6_snps_newick_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D6_snps_newick_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D_snps_newick_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01D_snps_newick_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01_snps_newick_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
-                <element name="Mbovis-01_snps_newick_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D6_snps_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D6_snps_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01D_snps_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/>
+                <element name="Mbovis-01_snps_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/>
             </output_collection>
         </test>
     </tests>