--- a/fastq_paired_end_joiner.xml	Mon Jan 27 09:25:44 2014 -0500
+++ b/fastq_paired_end_joiner.xml	Mon Jul 07 15:37:28 2014 -0400
@@ -1,12 +1,16 @@
-<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0">
+<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0">
   <description>on paired end reads</description>
   <requirements>
     <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
   </requirements>
-  <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file'</command>
+  <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command>
   <inputs>
     <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" />
     <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" />
+    <param name="style" type="select" label="FASTQ Header Style">
+      <option value="old" selected="true">old</option>
+      <option value="new">new</option>
+    </param>
   </inputs>
   <outputs>
     <data name="output_file" format="input" />
@@ -21,14 +25,19 @@
   <help>
 **What it does**
 
-This tool joins paired end FASTQ reads from two separate files into a single read in one file. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is excluded from the output.
-
-Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
+This tool joins paired end FASTQ reads from two separate files into a
+single read in one file.  The join is performed using sequence
+identifiers, allowing the two files to contain differing ordering.  If
+a sequence identifier does not appear in both files, it is excluded
+from the output.
 
 -----
 
 **Input formats**
 
+Both old and new (from recent Illumina software) style FASTQ headers
+are supported.  The following example uses the "old" style.
+
 Left-hand Read::
 
     @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1
@@ -56,10 +65,26 @@
 
 ------
 
-**Citation**
+**The "new" style**
+
+Recent Illumina FASTQ headers are structured as follows::
+
+  @COORDS FLAGS
+  COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y
+  FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE
+
+where the whitespace character between COORDS and FLAGS can be either
+a space or a tab.
 
-If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
+------
+
+**Credits**
 
+This is an extended version (adds support for "new" style FASTQ headers)
+of D. Blankenberg's fastq joiner:
 
+`Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
+
+New style header support added by Simone Leo &lt;simone.leo@crs4.it&gt;
   </help>
 </tool>