annotate parse_primersearch.xml @ 0:21053f7f9ed1 draft

First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
1 <?xml version="1.0"?>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
2 <tool id="parse_primersearch_1" name="Parse Primer search">
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
3 <description>Parse EMBOSS primer search output to tabular </description>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
4 <command interpreter="perl">parse_primersearch.pl $inputPrimersearchFile $outputfile </command>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
5 <inputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
6 <param format="primersearch" name="inputPrimersearchFile" type="data" label="Primersearch output file"/>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
7 </inputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
8 <outputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
9
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
10 <data format="tabular" name="outputfile" />
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
11 </outputs>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
12 <help>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
13
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
14 .. class:: infomark
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
15
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
16 **TIP**
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
17
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
18 This tool parses EMBOSS primersearch_ output into columnar format suitable for use as interval
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
19
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
20
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
21
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
22 Columns are:
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
23
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
24 1. Primer set ID
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
25 2. Hit ID
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
26 3. Number of mismatches
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
27 4. Amplimer start
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
28 5. Amplimer end
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
29 6. Amplicon length
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
30
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
31
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
32 ----
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
33
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
34 **Example**
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
35
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
36 *output*
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
37
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
38 ::
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
39
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
40 ACP032 isotig07062 0 214 363 149
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
41 ACP223 isotig04647 0 362 574 212
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
42 ACP224 isotig04647 0 303 519 216
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
43 ACP225 isotig04647 0 153 355 202
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
44 ACP363 isotig10393 0 93 193 100
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
45 ACP394 isotig00271 0 894 986 92
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
46 ACP394 isotig00273 0 805 897 92
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
47 ACP440 isotig05277 0 506 601 95
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
48 ACP615 isotig00271 0 894 978 84
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
49 ACP615 isotig00273 0 805 889 84
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
50 AJK295 isotig06005 0 182 651 469
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
51
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
52
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
53 .. _primersearch: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
54
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
55 -----------------------
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
56
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
57 *If you use this tool please cite:*
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
58
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
59 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
60 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
61 (2012)
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
62
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
63 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
64 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
65
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
66
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
67 </help>
21053f7f9ed1 First upload of PCR Marker tools
john-mccallum
parents:
diff changeset
68 </tool>