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comparison fastq_dump.xml @ 9:eb55ff614fed

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Fixed bug affecting --split-spot option.
author Matt Shirley <mdshw5@gmail.com>
date Fri, 25 Jul 2014 14:27:16 -0400
parents 558a88cd49e4
children 393a04ec0fa9
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8:558a88cd49e4 9:eb55ff614fed
1 <tool id="fastq_dump" name="Extract reads" version="1.1.1"> 1 <tool id="fastq_dump" name="Extract reads" version="1.1.2">
2 <description> from NCBI SRA.</description> 2 <description> from NCBI SRA.</description>
3 <command> 3 <command>
4 fastq-dump --log-level fatal 4 fastq-dump --log-level fatal
5 #if $input.input_select == "file": 5 #if $input.input_select == "file":
6 --accession '${input.file.name}' 6 --accession '${input.file.name}'
7 #else: 7 #else:
8 --accession $input.accession 8 --accession $input.accession
9 #end if 9 #end if
10 --defline-seq '@\$sn[_\$rn]/\$ri' 10 --defline-seq '@\$sn[_\$rn]/\$ri'
11 --stdout 11 --stdout
12 #if $split == "yes": 12 #if str( $split ) == "yes":
13 --split-spot 13 --split-spot
14 #end if 14 #end if
15 #if str( $alignments ) == "aligned": 15 #if str( $alignments ) == "aligned":
16 --aligned 16 --aligned
17 #end if 17 #end if