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comparison fastq_dump_paired.xml @ 9:f21bcc7ffacf draft default tip

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author mandorodriguez
date Thu, 17 Mar 2016 16:39:00 -0400
parents daebdda744fc
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8:daebdda744fc 9:f21bcc7ffacf
10 ## ! We only have a simple single command here. 10 ## ! We only have a simple single command here.
11 fastq-dump --log-level fatal --split-3 --accession ${accession_number} --ncbi_error_report never; 11 fastq-dump --log-level fatal --split-3 --accession ${accession_number} --ncbi_error_report never;
12 ls -lh | grep ${accession_number}; 12 ls -lh | grep ${accession_number};
13 mv -v ${accession_number}_1.fastq R1.fastq; 13 mv -v ${accession_number}_1.fastq R1.fastq;
14 mv -v ${accession_number}_2.fastq R2.fastq; 14 mv -v ${accession_number}_2.fastq R2.fastq;
15 echo "Deleting any stored files in ~/ncbi";
16 rm -rf ~/ncbi/*
17 </command> 15 </command>
18 <inputs> 16 <inputs>
19 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/> 17 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
20 </inputs> 18 </inputs>
21 <outputs> 19 <outputs>