Format file path

Author: RZ9082

tools/porechop/porechop.xml

@@ -8,8 +8,14 @@
     </requirements>
     <version_command>porechop --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+#import re
+
+#set file_path = re.sub('[^\s\w\-.]', '_', str($input_file.element_identifier))
+
+ln -s '$input_file' '$file_path' &&
+
 porechop
-    -i '$input_file'
+    -i '$file_path'
     --format '$format'
     --barcode_threshold '$barcode_binning_settings.barcode_threshold'
     --barcode_diff '$barcode_binning_settings.barcode_diff'