Mercurial > repos > matt-shirley > sra_tools

view sra_pileup.xml @ 29:d5f7232e67d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
debug prefetch caching and accession input for fastq_dump
author Matt Shirley <mdshw5@gmail.com>
date Sat, 29 Jun 2013 16:01:28 -0400
parents 4985f8c00366
children a0925f507352
line wrap: on
line source

<tool id="sra_pileup" name="Generate pileup format" version="1.0.0">
  <description> from NCBI sra.</description>
  <command>sra-pileup '$input' > $output</command>
  <version_string>sra-pileup --version</version_string>
  <inputs>
    <param format="sra" name="input" type="data" label="sra archive"/>
  </inputs>
  <outputs>
    <data format="sam" name="output"/>
  </outputs>
  <requirements>
    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
  </requirements>
  <help>
    !!! Note that this tool does not function correctly !!!
    This tool produces pileup format from sra archives using sra-pileup. 
    The sra-pileup 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>