Mercurial > repos > matt-shirley > sam_dump

annotate sam_dump.xml @ 2:39dab3a4578b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
bug fixes
author Matthew Shirley <mdshw5@gmail.com>
date Wed, 14 Nov 2012 16:55:35 -0500
parents d1dc85d3e490
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
d1dc85d3e490 Edited description and requirements.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
1 <tool id="sam_dump" name="Extract SAM" version="1.0.0">
d1dc85d3e490 Edited description and requirements.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
2 <description> format reads from NCBI SRA.</description>
2
39dab3a4578b bug fixes
Matthew Shirley <mdshw5@gmail.com>
parents: 1
diff changeset
3 <command>sam-dump $header $aligned $primary '$input' > $output</command>
0
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
4 <version_string>sam-dump --version</version_string>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
5 <inputs>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
6 <param format="sra" name="input" type="data" label="sra archive"/>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
7 <param format="text" name="header" type="select" value="">
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
8 <label>Output SAM header</label>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
9 <option value="--header">Yes</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
10 <option value="--no-header">No</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
11 </param>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
12 <param format="text" name="aligned" type="select" value="">
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
13 <label>Output unaligned reads</label>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
14 <option value="">No</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
15 <option value="--unaligned">Yes</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
16 </param>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
17 <param format="text" name="primary" type="select" value="">
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
18 <label>Output only primary aligments</label>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
19 <option value="">No</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
20 <option value="--primary">Yes</option>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
21 </param>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
22 </inputs>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
23 <outputs>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
24 <data format="sam" name="output"/>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
25 </outputs>
1
d1dc85d3e490 Edited description and requirements.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
26 <requirements>
d1dc85d3e490 Edited description and requirements.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
27 <requirement type="binary">sam-dump</requirement>
d1dc85d3e490 Edited description and requirements.
Matthew Shirley <mdshw5@gmail.com>
parents: 0
diff changeset
28 </requirements>
0
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
29 <help>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
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.
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
31 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
32 </help>
c2995e659548 First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.
mdshw5@gmail.com
parents:
diff changeset
33 </tool>