diff bismark_bowtie2_wrapper.xml @ 20:0895fe70075d draft

Uploaded

--- a/bismark_bowtie2_wrapper.xml	Thu Aug 14 04:46:12 2014 -0400
+++ b/bismark_bowtie2_wrapper.xml	Mon Jan 26 14:46:05 2015 -0500
@@ -7,19 +7,14 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="2.1.0">bowtie2</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
         
         ## 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
 
@@ -39,6 +34,7 @@
         ##  Input parameters
         ##
 
+
         #if $singlePaired.sPaired == "single":
             --single-paired $singlePaired.input_singles
 
@@ -62,17 +58,14 @@
             --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
@@ -282,22 +275,18 @@
             </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" and
-          params['settingsType'] == "custom" and
-          params['suppressed_read_file'] is True
-        ))
-      </filter>
+      <filter>singlePaired['sPaired'] == "paired"</filter>
+      <filter>params['settingsType'] == "custom"</filter>
+      <filter>params['supressed_read_file'] is True</filter>
       <actions>
         <conditional name="singlePaired.sPaired">
           <when value="single">
@@ -306,9 +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>
@@ -330,22 +319,18 @@
             </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" and
-          params['settingsType'] == "custom" and
-          params['unmapped_read_file'] is True
-        ))
-      </filter>
+      <filter>singlePaired['sPaired'] == "paired"</filter>
+      <filter>params['settingsType'] == "custom"</filter>
+      <filter>params['unmapped_read_file'] is True</filter>
       <actions>
         <conditional name="singlePaired.sPaired">
           <when value="single">
@@ -354,9 +339,9 @@
             </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>
@@ -656,7 +641,4 @@
                          always used and its default value is set to 10.
 
   </help>
-  <citations>
-      <citation type="doi">10.1093/bioinformatics/btr167</citation>
-  </citations>
 </tool>