# HG changeset patch
# User bgruening
# Date 1422301565 18000
# Node ID 0895fe70075de47b23e9135fc34e9a64a8c67ec6
# Parent  30caca800c9b17e17c7e2445ffd9fac0e29af33c
Uploaded

diff -r 30caca800c9b -r 0895fe70075d bismark_bowtie2_wrapper.xml
--- 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>
diff -r 30caca800c9b -r 0895fe70075d bismark_bowtie_wrapper.xml
--- 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>
diff -r 30caca800c9b -r 0895fe70075d bismark_methylation_extractor.xml
--- a/bismark_methylation_extractor.xml	Thu Aug 14 04:46:12 2014 -0400
+++ b/bismark_methylation_extractor.xml	Mon Jan 26 14:46:05 2015 -0500
@@ -13,7 +13,7 @@
 
         --infile $input
 
-        #--bismark_path \$SCRIPT_PATH
+        --bismark_path \$SCRIPT_PATH
 
         #if $singlePaired.sPaired == "single":
             --single-end
diff -r 30caca800c9b -r 0895fe70075d bismark_wrapper.py
--- a/bismark_wrapper.py	Thu Aug 14 04:46:12 2014 -0400
+++ b/bismark_wrapper.py	Mon Jan 26 14:46:05 2015 -0500
@@ -17,6 +17,7 @@
 
 def __main__():
 
+    print 'tempfile_location',tempfile.gettempdir()
     #Parse Command Line
     parser = argparse.ArgumentParser(description='Wrapper for the bismark bisulfite mapper.')
     parser.add_argument( '-p', '--num-threads', dest='num_threads',
@@ -257,6 +258,9 @@
 
     # Final bismark command:
     cmd = cmd % arguments
+    print 'bismark_cmd:', cmd
+    #sys.stderr.write( cmd )
+    #sys.exit(1)
     # Run
     try:
         tmp_out = tempfile.NamedTemporaryFile().name
@@ -317,8 +321,8 @@
         """
         #tmp_out = tempfile.NamedTemporaryFile( dir=output_dir ).name
         tmp_stdout = open( tmp_out, 'wab' )
-        #tmp_err = tempfile.NamedTemporaryFile( dir=output_dir ).name
-        tmp_stderr = open( tmp_err, 'wab' )
+        tmp_err = tempfile.NamedTemporaryFile( dir=output_dir ).name
+        tmp_stderr = open( tmp_err, 'wb' )
 
         tmp_res = tempfile.NamedTemporaryFile( dir= output_dir).name
 
@@ -334,22 +338,18 @@
             if returncode != 0:
                 raise Exception, open( tmp_stderr.name ).read()
         else:
-            tmp_res = bam_files[0]
+	    tmp_res = bam_files[0]
 
         bam_path = "%s" % tmp_res
 
         if os.path.exists( bam_path ):
-            if args.sort_bam:
-                cmd = 'samtools sort -@ %s %s sorted_bam' % (args.num_threads, bam_path)
-                proc = subprocess.Popen( args=shlex.split( cmd ) )
-                returncode = proc.wait()
-                if returncode != 0:
-                    raise Exception("Error during '%s'" % cmd)
-                shutil.move( 'sorted_bam.bam', args.output )
-            else:
-                shutil.move( bam_path, args.output )
+	    if args.sort_bam:
+                cmd = 'samtools sort -@ %s %s %s' % (args.num_threads, bam_path, args.output) 
+	    else:
+                shutil.copy( bam_path, args.output )
         else:
             stop_err( 'BAM file no found:\n' + str( bam_path ) )
+		
 
 
     # TODO: look for errors in program output.