Mercurial > repos > matt-shirley > sra_tools

annotate sra_fetch.xml @ 18:384f93a14b47 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
try static build to resolve missing libraries
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 21:22:17 -0400
parents 078b8e168b0c
children d850324e82cf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
078b8e168b0c update tool wrapper and increment version
Matt Shirley <mdshw5@gmail.com>
parents: 13
diff changeset
1 <tool id="sra_fetch" name="Fetch SRA" version="1.0.2">
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>
15
078b8e168b0c update tool wrapper and increment version
Matt Shirley <mdshw5@gmail.com>
parents: 13
diff changeset
3 <command interpreter="python">sra_fetch.py --accession '$accession' --out '$output'</command>
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
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:
diff changeset
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>