Mercurial > repos > matt-shirley > sra_tools
diff fastq_dump.xml @ 22:423f3eb06428 draft
more fixes for sra datatype, added sra_pileup
| author | Matt Shirley <mdshw5@gmail.com> |
|---|---|
| date | Wed, 19 Jun 2013 14:11:37 -0400 |
| parents | d850324e82cf |
| children | 5f57967aac3e |
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--- a/fastq_dump.xml Wed Jun 19 13:31:58 2013 -0400 +++ b/fastq_dump.xml Wed Jun 19 14:11:37 2013 -0400 @@ -1,9 +1,9 @@ <tool id="fastq_dump" name="Extract fastq" version="1.0.2"> - <description> format reads from NCBI SRA.</description> + <description> format reads from NCBI sra.</description> <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command> <version_string>fastq-dump --version</version_string> <inputs> - <param format="SRA" name="input" type="data" label="sra archive"/> + <param format="sra" name="input" type="data" label="sra archive"/> <param format="text" name="split" type="select" value=""> <label>Split read pairs</label> <option value="">No</option> @@ -26,6 +26,8 @@ <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> - This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + This tool extracts fastq format reads from sra archives using fastq-dump. + The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> </tool>