Mercurial > repos > matt-shirley > sra_tools
annotate sra_fetch.xml @ 0:cdcc400dcafc draft
Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
author | matt-shirley <mdshw5@gmail.com> |
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date | Tue, 27 Nov 2012 13:31:09 -0500 |
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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
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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> |