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annotate sra_fetch.xml @ 0:cdcc400dcafc draft

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Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
author matt-shirley <mdshw5@gmail.com>
date Tue, 27 Nov 2012 13:31:09 -0500
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cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
1 <tool id="sra_fetch" name="Fetch SRA" version="1.0.0">
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
2 <description> by accession from NCBI SRA.</description>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
3 <command interpreter="python">sra_fetch.py '$accession' '$output'</command>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
4 <inputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
5 <param name="accession" size="13" type="text" value="SRR000001" label="SRA run accession"/>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
6 </inputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
7 <outputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
8 <data format="sra" name="output" label="Fetch ${accession.value}"/>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
9 </outputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
10 <requirements>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
11 <requirement type="python">sra_fetch.py</requirement>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
12 </requirements>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
13 <help>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
14 This tool fetches SRA archives from NCBI over FTP using the python ftplib.
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
15 </help>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
diff changeset
16 </tool>