diff bwa-mem.xml @ 5:fbf460831036 draft

planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty

--- a/bwa-mem.xml	Thu Jun 18 17:35:40 2015 -0400
+++ b/bwa-mem.xml	Tue Jul 21 13:51:02 2015 -0400
@@ -1,7 +1,8 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.2.2">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
+    <import>read_group_macros.xml</import>
     <import>bwa_macros.xml</import>
   </macros>
   <requirements>
@@ -103,7 +104,16 @@
 
     #end if
 
-    #if str( $rg.rg_selector ) == "set":
+    ## Handle read group options...
+    @define_read_group_helpers@
+    #if str( $fastq_input.fastq_input_selector ) == "paired":
+      #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
+    #else:
+      #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
+    #end if
+    @set_use_rg_var@
+    @set_read_group_vars@
+    #if $use_rg
       @set_rg_string@
       -R '$rg_string'
     #end if
@@ -189,7 +199,7 @@
       </when>
     </conditional>
 
-    <expand macro="readgroup_params" />
+    <expand macro="read_group_conditional" />
 
     <conditional name="analysis_type">
       <param name="analysis_type_selector" type="select" label="Select analysis mode">