1<multi-test> 2 <remove-temp-dir url="bwa4"/> 3 <create-temp-dir url="bwa4"/> 4 <run-cmdline 5 task="!common_data_dir!bwa/workflow/bwa.uwl" 6 in="!common_data_dir!reads/e_coli_1000_1.fa" 7 out_dir="!tmp_data_dir!bwa4" 8 ref="!common_data_dir!bwa/index/ecoli.fa" 9 use-miss-prob="false" 10 max-diff="5" 11 index-alg="is" 12 seed-length="10" 13 max-gap="6" 14 best-hits="30" 15 scaled-gap="true" 16 non-iterative="false" 17 enable-long-gaps="false" 18 indel-offset="2" 19 long-deletions="7" 20 max-queue="1000000" 21 barcode-length="2" 22 num-threads="2" 23 max-seed="1" 24 mistmatch-penalty="2" 25 gap-open-penalty="9" 26 gap-ext-penalty="7" 27 quality-threshold="4" 28 /> 29 <compare-sam-by-length file1="bwa4/bwa/out.sam" file2="bwa/aln_pattern/max_diff/ecoli_1_is_all_params.sam"/> 30 <remove-temp-dir url="bwa4"/> 31</multi-test> 32