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view sra_validate.xml @ 37:4da2d7f0128e draft

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Exposed more options for fastq_dump and sam_dump
author Matt Shirley <mdshw5@gmail.com>
date Thu, 01 Aug 2013 13:57:27 -0400
parents 7e033744cb20
children
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<tool id="sra_validate" name="Validate sra" version="1.0.2">
  <description> and report any errors.</description>
  <command>vdb-validate -md5 '$input' 2> $output </command>
  <version_string>vdb-validate --version</version_string>
  <inputs>
    <param format="sra" name="input" type="data" label="sra archive"/>
  </inputs>
  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <stdio>
    <exit_code range="127" level="fatal" description="Cannot find vdb-validate binary"/>
  </stdio>
  <requirements>
    <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
  </requirements>
  <help>
    This tool checks the data integrity of an sra archive using vdb-validate. 
    The vdb-validate 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>