Mercurial > repos > john-mccallum > pcr_markers

comparison convert_gsMapper_gff3.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="gsMapper_to_gff3_1" name="Convert gsMapper to gff3">
3 <description>Convert Roche gsMapper to GFF3</description>
4 <command interpreter="bash">gsmapper2gff.sh $inputGsFile $outputfile</command>
5 <inputs>
6 <param format="txt" name="inputGsFile" type="data" label="Roche gsMapper 454HCDiffs.txt or 454AllDiffs.txt file"/>
7
8 </inputs>
9 <outputs>
10 <data format="gff3" name="outputfile" />
11 </outputs>
12 <help>
13 .. class:: infomark
14
15 **TIP**
16
17 This tool parses Roche gsMapper read mapping output into GVF/GFF3 format
18
19
20 ----
21
22 **Example**
23
24 *input*
25
26 ::
27
28 >Reference Start End Ref Var Total Var Ref Var Coding Region Known # Fwd # Rev # Fwd # Rev
29 >Accno Pos Pos Nuc Nuc Depth Freq AA AA Frame Name SNP's w/ var w/ var Total Total
30 ______________________________
31
32 >1118212 673 673 A C 7 100% 6 1 6 1
33
34 Reads with Difference:
35 1118212 648+ GTTGGTCCACTATTACTCTCAGATT-ATTTCATAACAATAATGG----A-TAC-AA 696
36 **
37 FX289JP01DVQR7 53- GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGGGCTGA-TACTA 1
38 FX289JP02IJT2O (7) 82+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 130
39 FX289JP01B8R7V 84+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATA-TGG----A-TAC-AA 131
40 FX289JP02FX58L 68+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----AC-AC-AA 116
41 FX289JP02JXAX7 (7) 67+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 115
42 FX289JP02JOOQZ (2) 69+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 117
43 FX289JP02GPHPX 45+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 93
44 **
45
46
47 *output*
48
49 ::
50
51 ##gff-version 3
52 1118212 gsMapper SNP 673 673 . . . ID=1118212:gsMapper:SNP:673;Reference_seq=A;Variant_seq=C;Total_reads=7;Variant_freq=100;
53 1118212 gsMapper SNP 730 730 . . . ID=1118212:gsMapper:SNP:730;Reference_seq=A;Variant_seq=G;Total_reads=13;Variant_freq=31;
54 1118212 gsMapper SNP 782 782 . . . ID=1118212:gsMapper:SNP:782;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_freq=92;
55 1118212 gsMapper SNP 1319 1319 . . . ID=1118212:gsMapper:SNP:1319;Reference_seq=G;Variant_seq=A;Total_reads=7;Variant_freq=100;
56
57 -----------------------
58
59 *If you use this tool please cite:*
60
61 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
62 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
63 (2012)
64
65 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
66 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
67
68
69 </help>
70 </tool>