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comparison fastq_dump.xml @ 8:558a88cd49e4

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bump toolkit versions, old registration path
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:11:04 -0400
parents 293927a46697
children eb55ff614fed
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7:e724bff23fb6 8:558a88cd49e4
1 <tool id="fastq_dump" name="Extract reads" version="1.1.1"> 1 <tool id="fastq_dump" name="Extract reads" version="1.1.1">
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 $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
18 #if str( $alignments ) == "unaligned": 18 #if str( $alignments ) == "unaligned":
19 --unaligned 19 --unaligned
20 #end if 20 #end if
21 #if str( $minID ) != "": 21 #if str( $minID ) != "":
22 --minSpotId $minID 22 --minSpotId $minID
23 #end if 23 #end if
24 #if str( $maxID ) != "": 24 #if str( $maxID ) != "":
25 --maxSpotId $maxID 25 --maxSpotId $maxID
26 #end if 26 #end if
27 #if str( $minlen ) != "": 27 #if str( $minlen ) != "":
28 --minReadLen $minlen 28 --minReadLen $minlen
29 #end if 29 #end if
30 #if str( $readfilter ) != "": 30 #if str( $readfilter ) != "":
31 --read-filter $readfilter 31 --read-filter $readfilter
32 #end if 32 #end if
33 #if str( $region ) != "": 33 #if str( $region ) != "":
34 --aligned-region $region 34 --aligned-region $region
35 #end if 35 #end if
36 #if str( $spotgroups ) != "": 36 #if str( $spotgroups ) != "":
46 --fasta 46 --fasta
47 #end if 47 #end if
48 #if $input.input_select=="file": 48 #if $input.input_select=="file":
49 $input.file 49 $input.file
50 #else: 50 #else:
51 $input.accession 51 $input.accession
52 #end if 52 #end if
53 > $output 53 > $output
54 </command> 54 </command>
55 <version_string>fastq-dump --version</version_string> 55 <version_string>fastq-dump --version</version_string>
56 <inputs> 56 <inputs>
110 </outputs> 110 </outputs>
111 <stdio> 111 <stdio>
112 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> 112 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
113 </stdio> 113 </stdio>
114 <requirements> 114 <requirements>
115 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> 115 <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
116 </requirements> 116 </requirements>
117 <help> 117 <help>
118 This tool extracts reads from SRA archives using fastq-dump. 118 This tool extracts reads from SRA archives using fastq-dump.
119 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 119 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
120 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. 120 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
121 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 121 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
122 </help> 122 </help>
123 </tool> 123 </tool>