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annotate sra_validate.xml @ 38:a0925f507352 draft

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bring pileup to parity with sam; fixed minMapq for sam
author Matt Shirley <mdshw5@gmail.com>
date Sun, 04 Aug 2013 23:17:53 -0400
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1 <tool id="sra_validate" name="Validate sra" version="1.0.2">
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2 <description> and report any errors.</description>
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3 <command>vdb-validate -md5 '$input' 2> $output </command>
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4 <version_string>vdb-validate --version</version_string>
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5 <inputs>
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6 <param format="sra" name="input" type="data" label="sra archive"/>
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7 </inputs>
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8 <outputs>
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9 <data format="txt" name="output"/>
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10 </outputs>
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11 <stdio>
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12 <exit_code range="127" level="fatal" description="Cannot find vdb-validate binary"/>
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13 </stdio>
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14 <requirements>
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15 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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16 </requirements>
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17 <help>
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18 This tool checks the data integrity of an sra archive using vdb-validate.
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19 The vdb-validate program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
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20 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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21 </help>
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22 </tool>