--- a/bwa.xml	Fri Mar 20 12:21:16 2015 -0400
+++ b/bwa.xml	Thu Jun 18 17:35:40 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="0.2.1">
+<tool id="bwa" name="Map with BWA" version="0.2.3">
   <description>- map short reads (&lt; 100 bp) against reference genome</description>
   <macros>
     <import>bwa_macros.xml</import>
@@ -24,7 +24,7 @@
       #end if
 
       #if str( $analysis_type.L ):
-        -B ${analysis_type.L}
+        -L ${analysis_type.L}
       #end if
     #end if
     </token>
@@ -250,11 +250,11 @@
   </command>
 
   <inputs>
-
+    
     <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Load reference genome from">
-        <option value="cached">Local cache</option>
-        <option value="history">History</option>
+      <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
+        <option value="cached">Use a built-in genome index</option>
+        <option value="history">Use a genome from history and build index</option>
       </param>
       <when value="cached">
         <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
@@ -387,6 +387,7 @@
       <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
       <param name="rg_selector" value="set"/>
       <param name="ID" value="rg1"/>
+      <param name="PL" value="CAPILLARY"/>
       <param name="analysis_type_selector" value="illumina"/>
       <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2" />
     </test>
@@ -394,18 +395,32 @@
   <help>
 **What is does**
 
-BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use BWA-MEM algorithm distributed as separate Galaxy tool.
+BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use BWA-MEM algorithm distributed as a separate Galaxy tool.
 
 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
 
-  - bwa aln - actual mapper placing reads onto the reference sequence
-  - bwa samse - post-processor converting suffix array coordinates into genome coordinates in SAM format for single reads
-  - bam sampe - post-processor for paired reads
+  - **bwa aln** - actual mapper placing reads onto the reference sequence
+  - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for single reads
+  - **bam sampe** - post-processor for paired reads
 
 Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM (not SAM; in reality SAM produced by the bwa is converted to BAM on the fly by samtools view command) format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
 
 -----
 
+**Indices: Selecting reference genomes for BWA**
+
+Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
+
+  1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.  
+  2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa aln`.
+    
+If your genome of interest is not listed here you have two choices:
+
+  1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
+  2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
+
+-----
+
 **Galaxy-specific option**
 
 Galaxy allows three levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are: