Mercurial > repos > john-mccallum > pcr_markers

comparison GVF_Features_Extracter.xml @ 0:21053f7f9ed1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:21053f7f9ed1
1 <?xml version="1.0"?>
2 <tool id="GVF Features Extracter_1" name="GVF Feature ID Extracter">
3 <description>Extract unique feature IDs from a GVF/GFF3 file </description>
4 <command >awk '!/^#/ {print $1":"$2":"$3":"$4}' $inputgff3File | sort | uniq > $column_outputfile</command>
5 <inputs>
6 <param format="gff3" name="inputgff3File" type="data" label="GVF/Gff3 File"/>
7 </inputs>
8 <outputs>
9 <data format="tabular" name="column_outputfile" />
10 </outputs>
11 <help>
12
13 .. class:: infomark
14
15 **TIP**
16
17 This tool extracts a unique feature identifier from GVF/GFF3 format, primarily to enable downstream analysis of SNPs or marker design
18
19
20 ----
21
22 **Example**
23
24 *input GFF3*
25
26 ::
27
28 ##gff-version 3
29 1119927 gsMapper SNP 434 434 . . . ID=1119927:gsMapper:SNP:434;Reference_seq=G;Variant_seq=A;Total_reads=10;Variant_freq=100;Enzyme=AluI;Phase=variant
30 1120709 gsMapper SNP 361 361 . . . ID=1120709:gsMapper:SNP:361;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_freq=68;Enzyme=TaqI;Phase=variant
31 1120709 gsMapper SNP 704 704 . . . ID=1120709:gsMapper:SNP:704;Reference_seq=A;Variant_seq=G;Total_reads=20;Variant_freq=90;Enzyme=RsaI;Phase=variant
32
33 *output tabular text*
34
35 ::
36
37 1119927:gsMapper:SNP:434
38 1120709:gsMapper:SNP:361
39 1120709:gsMapper:SNP:704
40
41 -----------------------------------------------------
42
43 *If you use this tool please cite:*
44
45 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
46 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
47 (2012)
48
49 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
50 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
51
52 </help>
53
54 </tool>