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