replace ln -s with cp

Author: hechth

tools/msconvert/msconvert_macros.xml

@@ -12,11 +12,11 @@
     #set basename = $re.sub(r'[^\w ,.\-+]','_',$input.element_identifier)
 
     #if $ext == 'wiff':
-      ln -s '${input.extra_files_path}/wiff' '${basename}.wiff' &&
-      ln -s '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
+      cp '${input.extra_files_path}/wiff' '${basename}.wiff' &&
+      cp '${input.extra_files_path}/wiff_scan' '${basename}.wiff.scan' &&
       #set inputmask = "'"+$basename+"'"
     #elif $ext.endswith('tar'):
-      ln -s '$input' '${basename}' &&
+      cp '$input' '${basename}' &&
       tar xf '${basename}' &&
       #set basename = $os.path.splitext($basename)[0]
       #if $ext.startswith('waters'):
@@ -29,14 +29,14 @@
         #raise RuntimeError("Unrecognized type of tar (${ext})")
       #end if
     #else
-      ln -s '$input' '${basename}' &&
+      cp '$input' '${basename}' &&
       #set inputmask = "'"+$basename+"'"
     #end if
 
     #if $data_processing.precursor_refinement.use_mzrefinement == "true"
       #set input_ident_name = ".".join((os.path.splitext($basename)[0], $data_processing.precursor_refinement.input_ident.ext))
       #set output_refinement_name = os.path.splitext($basename)[0] + '.mzRefinement.tsv'
-      ln -s '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
+      cp '$data_processing.precursor_refinement.input_ident' '$input_ident_name' &&
     #end if
 
     ## CAN_SUDO is "" if successful and "1" otherwise