--- a/bismark_bowtie2_wrapper.xml	Mon Apr 14 16:43:14 2014 -0400
+++ b/bismark_bowtie2_wrapper.xml	Mon Feb 09 18:24:41 2015 -0500
@@ -7,14 +7,20 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="2.1.0">bowtie2</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
-        
+
         ## Change this to accommodate the number of threads you have available.
         --num-threads "\${GALAXY_SLOTS:-24}"
 
-        --bismark_path \$SCRIPT_PATH
+        ##--bismark_path \$SCRIPT_PATH
 
         --bowtie2
 
@@ -34,7 +40,6 @@
         ##  Input parameters
         ##
 
-
         #if $singlePaired.sPaired == "single":
             --single-paired $singlePaired.input_singles
 
@@ -58,14 +63,17 @@
             --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
@@ -89,7 +97,7 @@
             --seed-extention-attempts $params.seed_extention_attempts
             ## default 2
             --max-reseed $params.max_reseed
-            
+
             ## default 70
             ##--maqerr $params.maqerr
 
@@ -140,6 +148,7 @@
         #end if
       #end if
 
+]]>
     </command>
     <inputs>
         <conditional name="refGenomeSource">
@@ -213,7 +222,7 @@
                 <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 -->
       <!--
@@ -275,18 +284,22 @@
             </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>
 
     <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['supressed_read_file'] is True</filter>
+      <filter>
+        ((
+            singlePaired['sPaired'] == "paired" and
+          params['settingsType'] == "custom" and
+          params['suppressed_read_file'] is True
+        ))
+      </filter>
       <actions>
         <conditional name="singlePaired.sPaired">
           <when value="single">
@@ -295,9 +308,9 @@
             </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>
@@ -319,18 +332,22 @@
             </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>
 
     <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['unmapped_read_file'] is True</filter>
+      <filter>
+        ((
+            singlePaired['sPaired'] == "paired" and
+          params['settingsType'] == "custom" and
+          params['unmapped_read_file'] is True
+        ))
+      </filter>
       <actions>
         <conditional name="singlePaired.sPaired">
           <when value="single">
@@ -339,9 +356,9 @@
             </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>
@@ -352,6 +369,7 @@
     </tests>
 
     <help>
+<![CDATA[
 
 **What it does**
 
@@ -409,8 +427,8 @@
     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
@@ -422,12 +440,12 @@
   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.
 
@@ -484,7 +502,7 @@
   --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.
@@ -496,7 +514,7 @@
 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
@@ -634,11 +652,15 @@
                          Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
                          can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
                          happens first. Only the best alignment is reported. Information from the other alignments is used to
-                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 
+                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
                          Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
                          aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
                          guarantee that the alignment reported is the best possible in terms of alignment score. -M is
                          always used and its default value is set to 10.
 
+]]>
   </help>
+  <citations>
+      <citation type="doi">10.1093/bioinformatics/btr167</citation>
+  </citations>
 </tool>