Extracting Genomic DNA can now result in an interval file with the

sequence appended as a new column.

tools/extract/fasta-subseq-wrapper.pl

@@ -18,7 +18,7 @@ my %seen = ();
 my @locFields = ();
 my %seqLocation = ();
 
-die "Cannot fetch sequences for unspecified genome\n" unless @ARGV == 11;
+die "Cannot fetch sequences for unspecified genome\n" unless @ARGV == 13;
 die "Please specify genome build by clicking on pencil icon in the original dataset\n" if $ARGV[10] =~ m/\?/;
 
 # Read /depot/data2/galaxy/alignseq.loc
@@ -47,7 +47,7 @@ if ($ARGV[8] > 0) {
 	$ARGV[8] = 1000000;
 }
 
-
+$ARGV[12] = int($ARGV[12]);
 
 open (BED,  "<$ARGV[1]") or die "Cannot open $ARGV[1] for reading :$!\n";
 open (FASTA,">$ARGV[3]") or die "Cannot open $ARGV[3] for writing :$!\n";
@@ -64,13 +64,19 @@ while (<BED>) {
 	  if (-e "$seqLocation{$ARGV[10]}$columns[$ARGV[5]].nib") {
 	    $call = "fasta-subseq $seqLocation{$ARGV[10]}$columns[$ARGV[5]].nib ".($columns[$ARGV[6]]+1)." $columns[$ARGV[7]] $columns[$ARGV[8]]"; #+1 to start position to fix coordinate system
 	    open (GET_SUBSEQ, "$call |") or die "Cannot start fasta-subseq:$!\n";
+	    my $seq = "";
 	    while (<GET_SUBSEQ>) {
 	      if (!m/\>/) {  # unless header print seq
-		print FASTA;
+		if ($ARGV[12]) {
+		  chomp $_;
+		  $seq = $seq . $_; }
+		else {
+		  print FASTA; }
 	      } else { # if header replace with seqdata
-		print FASTA ">$ARGV[10]_$columns[$ARGV[5]]_$columns[$ARGV[6]]_$columns[$ARGV[7]]_$columns[$ARGV[8]]\n";
+		if (!($ARGV[12])) { print FASTA ">$ARGV[10]_$columns[$ARGV[5]]_$columns[$ARGV[6]]_$columns[$ARGV[7]]_$columns[$ARGV[8]]\n"; }
 	      }
 	    }
+	    if ($ARGV[12]) { print FASTA join("\t",@columns) . "\t$seq\n"; }
 	    close (GET_SUBSEQ);
 	  } else {
 	    push (@errors, "Sequence $columns[$ARGV[5]] was not found for genome build $ARGV[10]\nMost likely your data lists wrong chromosome number for this organism\nCheck your genome build selection");

tools/extract/fasta-subseq-wrapper.xml

@@ -1,15 +1,21 @@
 <tool id="Extract genomic DNA 1" name="Extract genomic DNA">
   <description>using coordinates from assembled genomes</description>
-  <command interpreter="perl">fasta-subseq-wrapper.pl -i $input -o $out_file1 -p $input_chromCol $input_startCol $input_endCol $input_strandCol -g $dbkey</command>
+  <command interpreter="perl">fasta-subseq-wrapper.pl -i $input -o $out_file1 -p $input_chromCol $input_startCol $input_endCol $input_strandCol -g $dbkey -f $out_format</command>
   <inputs>
     <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"/>
+	<param name="out_format" type="select" label="Output Type">
+	<option value="0">FASTA</option>
+	<option value="1">Interval</option>
+	</param>
   </inputs>
   <outputs>
     <data format="fasta" name="out_file1" />
   </outputs>
+  <code file="fasta-subseq-wrapper_code.py" />
   <tests>
     <test>
       <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
+      <param name="out_format" value="0"/>
       <output name="out_file1" file="fsa_extract_genomic_dna.dat" />
     </test>
   </tests>

tools/extract/fasta-subseq-wrapper_code.py

@@ -0,0 +1,5 @@
+#Change format from FASTA to Interval if needed; use metadata from input file
+def exec_before_job(app, inp_data, out_data, param_dict, tool):
+    if param_dict['out_format'] == "1":
+        out_data['out_file1'].change_datatype('interval')
+        out_data['out_file1'].init_meta( copy_from=inp_data['input'] )