pcr_markers: parse_primersearch.xml annotate

annotate parse_primersearch.xml @ 3:402c3f0fe807 draft

Uploaded revised vcf_gff.py from Github to fix bug

author	john-mccallum
date	Thu, 18 Oct 2012 17:54:38 -0400
parents	21053f7f9ed1
children

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>

Mercurial > repos > john-mccallum > pcr_markers

annotate parse_primersearch.xml @ 3:402c3f0fe807 draft