Mercurial > repos > mandorodriguez > fastqdump_paired

comparison fastq_dump_paired.xml @ 5:86e30bb1e54e draft

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author mandorodriguez
date Thu, 21 Jan 2016 12:20:24 -0500
parents 6c9eb322892d
children aadca684d7c5
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4:6c9eb322892d 5:86e30bb1e54e
6 </requirements> 6 </requirements>
7 <command> 7 <command>
8 ## The command is a Cheetah template which allows some Python based syntax. 8 ## The command is a Cheetah template which allows some Python based syntax.
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces 9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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}; 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 </command> 15 </command>
16 <inputs> 16 <inputs>