--- a/bismark_bowtie_wrapper.xml	Mon Apr 14 16:43:14 2014 -0400
+++ b/bismark_bowtie_wrapper.xml	Mon Feb 09 18:24:41 2015 -0500
@@ -7,11 +7,17 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="0.12.8">bowtie</requirement>
     </requirements>
-    <parallelism method="basic"></parallelism>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <command interpreter="python">
+<![CDATA[
         bismark_wrapper.py
 
-        --bismark_path \$SCRIPT_PATH
+        ##--bismark_path \$SCRIPT_PATH
 
         ##
         ## Bismark Genome Preparation, if desired.
@@ -53,14 +59,17 @@
             --mate1 #echo ','.join($mate1)
             --mate2 #echo ','.join($mate2)
 
-            #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
-                --phred64-quals
-                --fastq
-            #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
-                --fastq
-            #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
-                --fasta
-            #end if
+            #for $mate_pair in $singlePaired.mate_list:
+                #if $mate_pair.input_mate1.ext == "fastqillumina":
+                    --phred64-quals
+                    --fastq
+                #elif $mate_pair.input_mate1.ext == "fastqsanger":
+                    --fastq
+                #elif $mate_pair.input_mate1.ext == "fasta":
+                    --fasta
+                #end if
+                #break
+            #end for
 
             -I $singlePaired.minInsert
             -X $singlePaired.maxInsert
@@ -123,6 +132,7 @@
         #end if
       #end if
 
+]]>
     </command>
     <inputs>
         <conditional name="refGenomeSource">
@@ -191,7 +201,7 @@
                 <!-- output Options -->
                 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
                 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
-                <!--end output options --> 
+                <!--end output options -->
             </when>  <!-- full -->
       </conditional>  <!-- params -->
       <!--
@@ -251,9 +261,9 @@
             </action>
           </when>
           <when value="paired">
-            <action type="format">
+            <!--action type="format">
               <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
-            </action>
+            </action-->
           </when>
         </conditional>
       </actions>
@@ -271,9 +281,9 @@
             </action>
           </when>
           <when value="paired">
-            <action type="format">
+            <!--action type="format">
               <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
-            </action>
+            </action-->
           </when>
         </conditional>
       </actions>
@@ -295,9 +305,9 @@
             </action>
           </when>
           <when value="paired">
-            <action type="format">
+            <!--action type="format">
               <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
-            </action>
+            </action-->
           </when>
         </conditional>
       </actions>
@@ -314,21 +324,20 @@
             </action>
           </when>
           <when value="paired">
-            <action type="format">
+            <!--action type="format">
               <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
-            </action>
+            </action-->
           </when>
         </conditional>
       </actions>
     </data>
-        
-        
     </outputs>
 
     <tests>
     </tests>
 
     <help>
+<![CDATA[
 
 **What it does**
 
@@ -386,8 +395,8 @@
     Column  Description
   --------  --------------------------------------------------------
   1  QNAME  seq-ID
-  2  FLAG   this flag tries to take the strand a bisulfite read 
-            originated from into account 
+  2  FLAG   this flag tries to take the strand a bisulfite read
+            originated from into account
             (this is different from ordinary DNA alignment flags!)
   3  RNAME  chromosome
   4  POS    start position
@@ -399,12 +408,12 @@
   10 SEQ    query SEQuence on the same strand as the reference
   11 QUAL   Phred33 scale
   12 NM-tag edit distance to the reference)
-  13 XX-tag base-by-base mismatches to the reference. 
+  13 XX-tag base-by-base mismatches to the reference.
             This does not include indels.
   14 XM-tag methylation call string
   15 XR-tag read conversion state for the alignment
   16 XG-tag genome conversion state for the alignment
-  
+
 
 Each read of paired-end alignments is written out in a separate line in the above format.
 
@@ -461,7 +470,7 @@
   --phred64-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
 
   --solexa-quals         Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
-                         (which can't). The formula for conversion is: 
+                         (which can't). The formula for conversion is:
                          phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
                          is usually the right option for use with (unconverted) reads emitted by the GA
                          Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
@@ -473,7 +482,7 @@
 Alignment::
 
   -n/--seedmms INT       The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
-                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 
+                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
                          default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
 
   -l/--seedlen           The "seed length"; i.e., the number of bases of the high quality end of the read to
@@ -546,5 +555,9 @@
                          the specified folder does not exist, Bismark will attempt to create it first. The path to the
                          temporary folder can be either relative or absolute.
 
+]]>
   </help>
+  <citations>
+      <citation type="doi">10.1093/bioinformatics/btr167</citation>
+  </citations>
 </tool>