Mercurial > repos > matt-shirley > sra_tools

annotate fastq_dump.xml @ 22:423f3eb06428 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
more fixes for sra datatype, added sra_pileup
author Matt Shirley <mdshw5@gmail.com>
date Wed, 19 Jun 2013 14:11:37 -0400
parents d850324e82cf
children 5f57967aac3e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
d850324e82cf fix datatype reference, increment versions
Matt Shirley <mdshw5@gmail.com>
parents: 20
diff changeset
1 <tool id="fastq_dump" name="Extract fastq" version="1.0.2">
22
423f3eb06428 more fixes for sra datatype, added sra_pileup
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
2 <description> format reads from NCBI sra.</description>
20
a1255154fa3f tweaks to fastq-dump command
Matt Shirley <mdshw5@gmail.com>
parents: 13
diff changeset
3 <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
0
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
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:
diff changeset
5 <inputs>
22
423f3eb06428 more fixes for sra datatype, added sra_pileup
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
6 <param format="sra" name="input" type="data" label="sra archive"/>
0
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
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:
diff changeset
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:
diff changeset
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:
diff changeset
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
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:
diff changeset
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 changeset
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:
diff changeset
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
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:
diff changeset
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 changeset
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
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:
diff changeset
25 <requirements>
11
cdba74ec9eca updated sra_toolkit dependency in <requirements>
Matt Shirley <mdshw5@gmail.com>
parents: 1
diff changeset
26 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
0
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
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:
diff changeset
28 <help>
22
423f3eb06428 more fixes for sra datatype, added sra_pileup
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
29 This tool extracts fastq format reads from sra archives using fastq-dump.
423f3eb06428 more fixes for sra datatype, added sra_pileup
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
30 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
423f3eb06428 more fixes for sra datatype, added sra_pileup
Matt Shirley <mdshw5@gmail.com>
parents: 21
diff changeset
31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
0
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
32 </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 changeset
33 </tool>