1<!-- Paired reads, two datasets -->
2<multi-test>
3    <remove-temp-dir url="bwa9"/>
4    <create-temp-dir url="bwa9"/>
5    <load-document index="doc" url="e_coli/e_coli_cut.fa" io="local_file" format="fasta"/>
6    <save-document doc="doc" url="bwa9/e_coli_cut.fa" io="local_file" format="fasta"/>
7    <run-cmdline
8            task="!common_data_dir!bwa/workflow/bwa-paired.uwl"
9            index="!tmp_data_dir!bwa9/e_coli_cut.fa"
10            sam-dir="!tmp_data_dir!bwa9"
11            reads1="!common_data_dir!e_coli/e_coli_reads/e_coli_1_1.fastq;;e_coli/e_coli_reads/e_coli_2_1.fastq"
12            reads2="!common_data_dir!e_coli/e_coli_reads/e_coli_1_2.fastq;;e_coli/e_coli_reads/e_coli_2_2.fastq"
13    />
14    <compare-sam-by-length file1="bwa9/bwa/out.sam" file2="bwa/workflow/paired1.sam"/>
15    <compare-sam-by-length file1="bwa9/bwa_1/out.sam" file2="bwa/workflow/paired2.sam"/>
16    <remove-temp-dir url="bwa9"/>
17</multi-test>
18