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? history 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) 0.04 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 (KS) 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