This is a pre-migration bwa. I've not updated this Galaxy instance, yet.

Here is a paste of used all options:

Will you select a reference genome from your history or use a built-in index?   
Select a reference from history 3: StaphAureus_USA300_FPR3757 .fasta
Is this library mate-paired?    paired
Forward FASTQ file      4: FASTQ Groomer on data 1
Reverse FASTQ file      5: FASTQ Groomer on data 2
BWA settings to use     full
Maximum edit distance (aln -n)  0
Fraction of missing alignments given 2% uniform base error rate (aln -n)        
Maximum number of gap opens (aln -o)    1
Maximum number of gap extensions (aln -e)       -1
Disallow long deletion within [value] bp towards the 3'-end (aln -d)    16
Disallow insertion/deletion within [value] bp towards the end (aln -i)  5
Number of first subsequences to take as seed (aln -l)   -1
Maximum edit distance in the seed (aln -k)      2
Mismatch penalty (aln -M)       3
Gap open penalty (aln -O)       11
Gap extension penalty (aln -E)  4
Proceed with suboptimal alignments if there are no more than INT equally best 
hits. (aln -R)    None
Disable iterative search (aln -N)       False
Maximum number of alignments to output in the XA tag for reads paired properly 
(samse/sampe -n) 3
Maximum number of alignments to output in the XA tag for disconcordant read 
pairs (excluding singletons) (sampe -N)     10
Maximum insert size for a read pair to be considered as being mapped properly 
(sampe -a)        500
Maximum occurrences of a read for pairing (sampe -o)    100000
Specify the read group for this file? (samse/sampe -r)  yes
Read group identifier (ID). Each @RG line must have a unique ID. The value of ID 
is used in the RG tags of alignment records. Must be unique among all read 
groups in header section.    M0004_RG
Sequencing center that produced the read (CN)   
Description (DS)        
Date that run was produced (DT) 
Flow order (FO). The array of nucleotide bases that correspond to the 
nucleotides used for each flow of each read.       
The array of nucleotide bases that correspond to the key sequence of each read 
Library name (LB)       M0004_LB
Programs used for processing the read group (PG)        BWA
Predicted median insert size (PI)       
Platform/technology used to produce the reads (PL)      ILLUMINA
Platform unit (PU)      M0004_PU
Sample (SM)     M0004_SM
Suppress the header in the output SAM file      False

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