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