Mercurial > repos > matt-shirley > sra_tools
annotate fastq_dump.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="fastq_dump" name="Extract fastq" 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> format reads 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>./fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $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 <version_string>fastq-dump --version</version_string> |
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 <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
|
6 <param format="sra" name="input" type="data" label="sra archive"/> |
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 <param format="text" name="split" type="select" 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
|
8 <label>Split read pairs</label> |
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 <option value="">No</option> |
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 <option value="--split-spot">Yes</option> |
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 </param> |
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 <param format="text" name="aligned" type="select" 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
|
13 <label>Specify alignment</label> |
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 <option value="">All</option> |
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 <option value="--aligned">Only aligned</option> |
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 <option value="--unaligned">Only unaligned</option> |
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
|
17 </param> |
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
|
18 </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
|
19 <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
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20 <data format="fastqsanger" name="output"/> |
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
|
21 </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
|
22 <stdio> |
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
|
23 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/> |
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
|
24 </stdio> |
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
|
25 <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
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26 <requirement type="binary">fastq-dump</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
|
27 </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
|
28 <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
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29 This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
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
|
30 </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
|
31 </tool> |