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annotate sra_fetch.xml @ 4:8ce70ee5f335 draft

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Updated wrapper script. First version that should work properly.
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 13:13:32 -0500
parents abdb4762ebcb
children 20a054a7e2fd
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abdb4762ebcb Dummy file. Todo: write python script for fetching SRA from NCBI FTP site, based on file name directory structure.
Matthew Shirley <mdshw5@gmail.com>
parents:
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1 <tool id="sra_fetch" name="Fetch SRA" version="1.0.0">
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8ce70ee5f335 Updated wrapper script. First version that should work properly.
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2 <description> by accession from NCBI SRA.</description>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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3 <command interpreter="python">sra_fetch.py $accession > $output</command>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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4 <inputs>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
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5 <param name="accession" size="13" type="text" value="SRR000001" label="SRA run accession"/>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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6 </inputs>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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7 <outputs>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
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8 <data format="sra" name="output"/>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
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parents: 0
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9 </outputs>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
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10 <requirements>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
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11 <requirement type="python">sra_fetch.py</requirement>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
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parents: 0
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12 </requirements>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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13 <help>
8ce70ee5f335 Updated wrapper script. First version that should work properly.
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14 This tool fetches SRA archives from NCBI over FTP using the python ftplib.
8ce70ee5f335 Updated wrapper script. First version that should work properly.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
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15 </help>
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abdb4762ebcb Dummy file. Todo: write python script for fetching SRA from NCBI FTP site, based on file name directory structure.
Matthew Shirley <mdshw5@gmail.com>
parents:
diff changeset
16 </tool>