Add support for column ranges to Cut tool. Thank to John Chilton for this code.

tools/filters/cutWrapper.pl

@@ -9,6 +9,9 @@ my @in = ();
 my @out = ();
 my $command = "";
 my $field = 0;
+my $start = 0;
+my $end = 0;
+my $i = 0;
 
 # a wrapper for cut for use in galaxy
 # cutWrapper.pl [filename] [columns] [delim] [output]
@@ -20,6 +23,13 @@ foreach ( split /,/, $ARGV[1] ) {
   if (m/^c\d{1,}$/i) {
     push (@columns, $_);
     $columns[@columns-1] =~s/c//ig;
+  } elsif (m/^c\d{1,}-c\d{1,}$/i) {
+    ($start, $end)  = split(/-/, $_);
+    $start =~ s/c//ig;
+    $end =~ s/c//ig;
+    for $i ($start .. $end) {
+       push (@columns, $i); 
+    }
   }
 }
 

tools/filters/cutWrapper.xml

@@ -1,4 +1,4 @@
-<tool id="Cut1" name="Cut" version="1.0.1">
+<tool id="Cut1" name="Cut" version="1.0.2">
   <description>columns from a table</description>
   <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command>
   <inputs>
@@ -141,6 +141,12 @@
       <param name="input" value="1.bed"/>
       <output name="out_file1" file="eq-cut.dat"/>
     </test>
+    <test>
+      <param name="columnList" value="c1,c4,c2-c3" />
+      <param name="delimiter" value="T" />
+      <param name="input" value="1.bed" />
+      <output name="out_file1" file="eq-cut.dat" />
+    </test>
   </tests>
   <help>
 
@@ -191,6 +197,11 @@ Input dataset (six columns: c1, c2, c3, c4, c5, and c6)::
    + 0 gene1 chr1 
    + 0 gene2 chr2
 
+**cut** on columns "**c1-c3**" will return::
+
+   chr1 10   1000 
+   chr2 100  1500
+
 
 **cut** on columns "**c8,c7,c4**" will return::