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annotate sam_dump.xml @ 13:45031bbf6b27 draft

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better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
author Matt Shirley <mdshw5@gmail.com>
date Mon, 17 Jun 2013 16:17:33 -0400
parents cdba74ec9eca
children d850324e82cf
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13
45031bbf6b27 better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
Matt Shirley <mdshw5@gmail.com>
parents: 11
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1 <tool id="sam_dump" name="Extract SAM" version="1.0.1">
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matt-shirley <mdshw5@gmail.com>
parents:
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2 <description> format reads from NCBI SRA.</description>
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matt-shirley <mdshw5@gmail.com>
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3 <command>sam-dump $header $aligned $primary '$input' > $output</command>
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matt-shirley <mdshw5@gmail.com>
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4 <version_string>sam-dump --version</version_string>
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matt-shirley <mdshw5@gmail.com>
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5 <inputs>
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matt-shirley <mdshw5@gmail.com>
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6 <param format="sra" name="input" type="data" label="sra archive"/>
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matt-shirley <mdshw5@gmail.com>
parents:
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7 <param format="text" name="header" type="select" value="">
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matt-shirley <mdshw5@gmail.com>
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8 <label>Output SAM header</label>
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matt-shirley <mdshw5@gmail.com>
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9 <option value="--header">Yes</option>
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matt-shirley <mdshw5@gmail.com>
parents:
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10 <option value="--no-header">No</option>
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matt-shirley <mdshw5@gmail.com>
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11 </param>
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matt-shirley <mdshw5@gmail.com>
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12 <param format="text" name="aligned" type="select" value="">
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Matt Shirley <mdshw5@gmail.com>
parents: 0
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13 <label>Output unaligned reads as well as aligned reads</label>
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matt-shirley <mdshw5@gmail.com>
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14 <option value="">No</option>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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15 <option value="--unaligned">Yes</option>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
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16 </param>
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matt-shirley <mdshw5@gmail.com>
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17 <param format="text" name="primary" type="select" 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:
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18 <label>Output only primary aligments</label>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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19 <option value="">No</option>
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matt-shirley <mdshw5@gmail.com>
parents:
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20 <option value="--primary">Yes</option>
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matt-shirley <mdshw5@gmail.com>
parents:
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21 </param>
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matt-shirley <mdshw5@gmail.com>
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22 </inputs>
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matt-shirley <mdshw5@gmail.com>
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23 <outputs>
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matt-shirley <mdshw5@gmail.com>
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24 <data format="sam" name="output"/>
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25 </outputs>
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26 <requirements>
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cdba74ec9eca updated sra_toolkit dependency in <requirements>
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27 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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28 </requirements>
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29 <help>
ffdd41766195 Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
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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.
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matt-shirley <mdshw5@gmail.com>
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31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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32 </help>
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33 </tool>