Merge pull request #30 from LUMC/fixnames

Fix a bug where tar could not handle complex names

CHANGELOG.md

@@ -1,3 +1,7 @@
+version 1.9.0-dev
+-----------------
++ Fix a bug where tar would not open certain filenames.
+
 version 1.8.1
 -----------------
 + Fix a bug where input files with spaces could not be used.

shm_csr.xml

@@ -24,9 +24,8 @@
 		<![CDATA[
 		#import os
 		#set $input=os.path.basename($in_file.name)
-		ln -s "$in_file" "$input" &&
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
-			$__tool_directory__/wrapper.sh "$input"
+			$__tool_directory__/wrapper.sh "$in_file"
 			custom $out_file $out_file.files_path
 			"$input" "-" $functionality $unique
 			$naive_output_cond.naive_output $naive_output_ca $naive_output_cg

wrapper.sh

@@ -23,7 +23,7 @@ filter_unique_count=${18}
 class_filter=${19}
 empty_region_filter=${20}
 fast=${21}
-BASENAME=$(basename "$input")
+BASENAME=$(basename "$title")
 # Cut off .txz or .tgz suffix and also replace spaces with underscores.
 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}"
 NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_}