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annotate sra_fetch.xml @ 13:45031bbf6b27 draft

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better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 16:17:33 -0400
parents ffdd41766195
children 078b8e168b0c
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13
45031bbf6b27 better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
Matt Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
1 <tool id="sra_fetch" name="Fetch SRA" version="1.0.1">
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ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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2 <description> by accession from NCBI SRA.</description>
13
45031bbf6b27 better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
Matt Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
3 <command interpreter="python">sra_fetch.py '$accession' -o '$output'</command>
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ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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4 <inputs>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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5 <param name="accession" size="13" type="text" value="SRR000001" label="SRA run accession"/>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
6 </inputs>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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7 <outputs>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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8 <data format="sra" name="output" label="Fetch ${accession.value}"/>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
9 </outputs>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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10 <requirements>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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11 <requirement type="python">sra_fetch.py</requirement>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
12 </requirements>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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13 <help>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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14 This tool fetches SRA archives from NCBI over FTP using the python ftplib.
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
15 </help>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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16 </tool>