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comparison fastq_dump.xml @ 28:fdc981664a43

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Update to most recent GitHub version passing tests.
author Matt Shirley <mdshw5@gmail.com>
date Wed, 01 Apr 2015 12:35:38 -0400
parents 8be4f23d1018
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27:8be4f23d1018 28:fdc981664a43
1 <tool id="fastq_dump" name="Extract reads" version="1.1.2"> 1 <tool id="fastq_dump" name="Extract reads" version="1.1.2">
2 <description> from NCBI SRA.</description> 2 <description> in FASTQ/A format 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:
121 <param name="maxID" value="5"/> 121 <param name="maxID" value="5"/>
122 <output name="output" file="fastq_dump_result.fastq" ftype="fastq" /> 122 <output name="output" file="fastq_dump_result.fastq" ftype="fastq" />
123 </test> 123 </test>
124 </tests> 124 </tests>
125 <help> 125 <help>
126 This tool extracts reads from SRA archives using fastq-dump. 126 This tool extracts reads from sra archives using sam-dump.
127 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 127 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
128 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. 128 The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools
129 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 129 Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy.
130 </help> 130 </help>
131 </tool> 131 </tool>