1<multi-test>
2    <remove-temp-dir url="bowtie2_5"/>
3    <create-temp-dir url="bowtie2_5"/>
4    <load-document index="doc" url="/bowtie2/lambda_virus.fa" io="local_file" format="fasta"/>
5    <save-document doc="doc" url="_tempRef5.fa" io="local_file" format="fasta"/>
6    <run-cmdline
7            task="!common_data_dir!bowtie2/aligner_worker/bowtie2-aligner.uwl"
8            in="!common_data_dir!bowtie2/reads_1.fq"
9            out-dir="!tmp_data_dir!bowtie2_5"
10            ref="!tmp_data_dir!_tempRef5.fa"
11            mode="--local"
12            mismatches="0"
13            seed-length="20"
14            dpad="15"
15            gbar="4"
16            seed="0"
17    />
18    <compare-two-sams-by-length file1="bowtie2_5/bowtie/out.sam" file2="bowtie2/aligner_worker/pattern1_local.sam" file3="bowtie2/aligner_worker/pattern1_local_twin.sam"/>
19    <remove-temp-dir url="bowtie2_5"/>
20</multi-test>
21