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annotate sam_dump.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:
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1 <tool id="sam_dump" name="Extract SAM" 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:
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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:
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3 <command>sam-dump $header $aligned $primary '$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:
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4 <version_string>sam-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:
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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="header" 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>
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8 <label>Output SAM header</label>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
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9 <option value="--header">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:
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10 <option value="--no-header">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
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>Output unaligned reads</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="">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
15 <option value="--unaligned">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
16 </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
17 <param format="text" name="primary" 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
18 <label>Output only primary aligments</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
19 <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
20 <option value="--primary">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
21 </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
22 </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
23 <outputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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24 <data format="sam" 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
25 </outputs>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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26 <requirements>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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27 <requirement type="binary">sam-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
28 </requirements>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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29 <help>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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30 This tool extracts SAM format reads from SRA archives using sam-dump. The sam-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
31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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
32 </help>
cdcc400dcafc Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
matt-shirley <mdshw5@gmail.com>
parents:
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33 </tool>