diff bismark_bowtie_wrapper.xml @ 20:0895fe70075d draft

Uploaded

--- a/bismark_bowtie_wrapper.xml	Thu Aug 14 04:46:12 2014 -0400
+++ b/bismark_bowtie_wrapper.xml	Mon Jan 26 14:46:05 2015 -0500
@@ -7,16 +7,11 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="0.12.8">bowtie</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
+    <parallelism method="basic"></parallelism>
     <command interpreter="python">
         bismark_wrapper.py
 
-        ##--bismark_path \$SCRIPT_PATH
+        --bismark_path \$SCRIPT_PATH
 
         ##
         ## Bismark Genome Preparation, if desired.
@@ -58,17 +53,14 @@
             --mate1 #echo ','.join($mate1)
             --mate2 #echo ','.join($mate2)
 
-            #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
+            #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
 
             -I $singlePaired.minInsert
             -X $singlePaired.maxInsert
@@ -259,9 +251,9 @@
             </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>
@@ -279,9 +271,9 @@
             </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>
@@ -303,9 +295,9 @@
             </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>
@@ -322,13 +314,15 @@
             </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>
@@ -553,7 +547,4 @@
                          temporary folder can be either relative or absolute.
 
   </help>
-  <citations>
-      <citation type="doi">10.1093/bioinformatics/btr167</citation>
-  </citations>
 </tool>