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