Apply suggestions from code review

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

Author: nsoranzo

tools/condense_characters/condense_characters.xml

@@ -1,4 +1,4 @@
-<tool id="Condense characters1" name="Condense"  version="1.0.1">
+<tool id="Condense characters1" name="Condense"  version="1.0.1" profile="24.0">
     <description>consecutive characters</description>
     <command>
         perl $__tool_directory__/condense_characters.pl

tools/cummerbund/cummeRbund.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy0">
+<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy0" profile="24.0">
     <description>visualize Cuffdiff output</description>
     <macros>
         <import>cummeRbund_macros.xml</import>

tools/remove_beginning/remove_beginning.xml

@@ -1,7 +1,7 @@
-<tool id="Remove beginning1" name="Remove beginning" version="1.0.1">
+<tool id="Remove beginning1" name="Remove beginning" version="1.0.1" profile="24.0">
     <description>of a file</description>
     <command>
-        perl $__tool_directory__/remove_beginning.pl
+        perl '$__tool_directory__/remove_beginning.pl'
             "${input}"
             "${num_lines}"
             "${out_file1}"