--- a/bwa-mem.xml	Fri Mar 20 12:21:16 2015 -0400
+++ b/bwa-mem.xml	Thu Jun 18 17:35:40 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.2.1">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.2.2">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
     <import>bwa_macros.xml</import>
@@ -135,9 +135,9 @@
   <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">
@@ -162,7 +162,7 @@
       <when value="paired">
         <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
         <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
@@ -173,7 +173,7 @@
       </when>
       <when value="paired_collection">
         <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
@@ -181,7 +181,7 @@
       </when>
       <when value="paired_iv">
         <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standerd deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
@@ -193,9 +193,9 @@
 
     <conditional name="analysis_type">
       <param name="analysis_type_selector" type="select" label="Select analysis mode">
-        <option value="illumina">Simple Illumina mode</option>
-        <option value="pacbio">PacBio mode (-x pacbio)</option>
-        <option value="full">Full list of options</option>
+        <option value="illumina">1.Simple Illumina mode</option>
+        <option value="pacbio">2.PacBio mode (-x pacbio)</option>
+        <option value="full">3.Full list of options</option>
       </param>
       <when value="illumina">
         <!-- do nothing -->
@@ -302,6 +302,8 @@
       <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="LB" value="AARDVARK-1" />
       <param name="analysis_type_selector" value="illumina"/>
       <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
     </test>
@@ -322,6 +324,20 @@
 
 -----
 
+**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 mem`.
+    
+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 four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are: