--- a/bismark_bowtie2_wrapper.xml	Tue Dec 25 05:54:01 2012 -0500
+++ b/bismark_bowtie2_wrapper.xml	Fri Mar 01 13:39:22 2013 -0500
@@ -12,7 +12,7 @@
         bismark_wrapper.py
         
         ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
+        --num-threads 12
 
         --bismark_path \$SCRIPT_PATH
 
@@ -47,16 +47,23 @@
                 --fasta
             #end if
         #else:
-            --mate-paired 
-            --mate1 $singlePaired.input_mate1
-            --mate2 $singlePaired.input_mate2
+            --mate-paired
+            #set $mate1 = list()
+            #set $mate2 = list()
+            #for $mate_pair in $singlePaired.mate_list
+                $mate1.append( str($mate_pair.input_mate1) )
+                $mate2.append( str($mate_pair.input_mate2) )
+            #end for
 
-            #if $singlePaired.input_mate1.ext == "fastqillumina":
+            --mate1 #echo ','.join($mate1)
+            --mate2 #echo ','.join($mate2)
+
+            #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
                 --phred64-quals
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fastqsanger":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
                 --fastq
-            #elif $singlePaired.input_mate1.ext == "fasta":
+            #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
                 --fasta
             #end if
 
@@ -157,8 +164,10 @@
                 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
+                <repeat name="mate_list" title="Paired End Pairs" min="1">
+                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
+                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
+                </repeat>
                 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                 <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
             </when>
@@ -247,7 +256,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -267,7 +276,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -291,7 +300,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -310,7 +319,7 @@
           </when>
           <when value="paired">
             <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
+              <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
             </action>
           </when>
         </conditional>
@@ -353,6 +362,11 @@
 
  .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
 
+
+.. class:: warningmark
+
+Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
+
 ------
 
 **Input formats**
@@ -415,12 +429,7 @@
 
 **Bismark parameter list**
 
-This is an exhaustive list of Bismark options:
-
-------
-
-**OPTIONS**
-
+This is an exhaustive list of Bismark options.
 
 Input::