1<multi-test>
2    <remove-temp-dir url="bowtie2_7"/>
3    <create-temp-dir url="bowtie2_7"/>
4    <load-document index="doc" url="/bowtie2/lambda_virus.fa" io="local_file" format="fasta"/>
5    <save-document doc="doc" url="_tempRef7.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_2.fq"
9            out-dir="!tmp_data_dir!bowtie2_7"
10            ref="!tmp_data_dir!_tempRef7.fa"
11            mode="--local"
12            mismatches="0"
13            seed-length="10"
14            dpad="5"
15            gbar="3"
16            seed="0"
17            no-mixed="true"
18            no-discordant="false"
19            nofw="true"
20            norc="false"
21            no-overlap="true"
22            no-contain="false"
23    />
24    <compare-two-sams-by-length file1="bowtie2_7/bowtie/out.sam" file2="bowtie2/aligner_worker/pattern3_local.sam" file3="bowtie2/aligner_worker/pattern3_local_twin.sam"/>
25    <remove-temp-dir url="bowtie2_7"/>
26</multi-test>
27