Mercurial > repos > matt-shirley > sra_tools
annotate fastq_dump.xml @ 13:45031bbf6b27 draft
better sra_fetch code, compliant (?) datatype, updated dependencies in tool wrappers
author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 17 Jun 2013 16:17:33 -0400 |
parents | cdba74ec9eca |
children | a1255154fa3f |
rev | line source |
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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="fastq_dump" name="Extract fastq" 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> |
1 | 3 <command>fastq-dump --log-level fatal --report never --accession '${input.name}' --stdout $split $aligned '$input' > $output </command> |
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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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4 <version_string>fastq-dump --version</version_string> |
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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5 <inputs> |
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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6 <param format="sra" name="input" type="data" label="sra archive"/> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
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7 <param format="text" name="split" 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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8 <label>Split read pairs</label> |
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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9 <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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10 <option value="--split-spot">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:
diff
changeset
|
11 </param> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
|
12 <param format="text" name="aligned" 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:
diff
changeset
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13 <label>Specify alignment</label> |
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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changeset
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14 <option value="">All</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:
diff
changeset
|
15 <option value="--aligned">Only aligned</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:
diff
changeset
|
16 <option value="--unaligned">Only unaligned</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:
diff
changeset
|
17 </param> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
|
18 </inputs> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
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19 <outputs> |
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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20 <data format="fastqsanger" name="output"/> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
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21 </outputs> |
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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22 <stdio> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
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23 <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
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24 </stdio> |
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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25 <requirements> |
11
cdba74ec9eca
updated sra_toolkit dependency in <requirements>
Matt Shirley <mdshw5@gmail.com>
parents:
1
diff
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26 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> |
0
ffdd41766195
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matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
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27 </requirements> |
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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28 <help> |
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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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. |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
changeset
|
30 </help> |
ffdd41766195
Initial version - still need to test if datatype works correctly, and implement scripted download of SRA binaries.
matt-shirley <mdshw5@gmail.com>
parents:
diff
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31 </tool> |