changeset 17:b55c12d26066 draft

Uploaded

--- a/bwameth.xml	Wed Sep 14 07:25:18 2016 -0400
+++ b/bwameth.xml	Wed Sep 14 07:25:39 2016 -0400
@@ -4,6 +4,7 @@
     <requirement type="package" version="0.4.6">toolshed</requirement>
     <requirement type="package" version="1.2">samtools</requirement>
     <requirement type="package" version="0.7.12">bwa</requirement>
+    <requirement type="package" version="0.20">bwameth</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -12,19 +13,24 @@
     <regex match="Exception:" />
     <regex match="Exception :" />
   </stdio>
-  <command interpreter="python">
+  <version_command>bwameth.py --version</version_command>
+  <command>
 <![CDATA[
-    bwameth_wrapper.py 
-        -p "\${GALAXY_SLOTS:-4}"
-
     #if $referenceSource.source != "indexed":
-        --makeIndex $referenceSource.reference
+        mkdir index_dir &&
+        ln -s '$referenceSource.reference' index_dir/genome.fa &&
+        bwameth.py index index_dir/genome.fa &&
+        #set index="index_dir/genome.fa"
     #else
-        --premadeIndex $referenceSource.index.fields.path
+        #set index=$referenceSource.index.fields.path
     #end if
 
+    bwameth.py
+        -t "\${GALAXY_SLOTS:-4}"
+        --reference ${index}
+
     #if str($readGroup).strip() != "":
-        --readGroup "${readGroup}"
+        --read-group "${readGroup}"
     #end if
 
     #if $single_or_paired.single_or_paired_opts == 'single':
@@ -32,6 +38,7 @@
     #else:
         $single_or_paired.input_mate1 $single_or_paired.input_mate2
     #end if
+    | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" output
 ]]>
   </command>
   <inputs>