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annotate sra_pileup.xml @ 31:85e47f636e10 draft

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debug prefetch caching and accession input for fastq_dump
author Matt Shirley <mdshw5@gmail.com>
date Sun, 30 Jun 2013 11:12:31 -0400
parents 4985f8c00366
children a0925f507352
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.0.0">
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2 <description> from NCBI sra.</description>
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3 <command>sra-pileup '$input' > $output</command>
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4 <version_string>sra-pileup --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="sam" name="output"/>
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10 </outputs>
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11 <requirements>
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12 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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13 </requirements>
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14 <help>
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15 !!! Note that this tool does not function correctly !!!
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16 This tool produces pileup format from sra archives using sra-pileup.
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17 The sra-pileup 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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18 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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19 </help>
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20 </tool>