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annotate sra_fetch.xml @ 0:ffdd41766195 draft

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Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
author matt-shirley <mdshw5@gmail.com>
date Tue, 27 Nov 2012 13:44:28 -0500
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children 45031bbf6b27
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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:
diff changeset
1 <tool id="sra_fetch" name="Fetch SRA" version="1.0.0">
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
2 <description> by accession from NCBI SRA.</description>
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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3 <command interpreter="python">sra_fetch.py '$accession' '$output'</command>
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
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
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:
diff changeset
16 </tool>