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comparison design_primers.xml @ 0:21053f7f9ed1 draft

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First upload of PCR Marker tools
author john-mccallum
date Thu, 14 Jun 2012 19:29:26 -0400
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children a0689dc29b7f
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-1:000000000000 0:21053f7f9ed1
1 <?xml version="1.0"?>
2 <tool id="Genetic_Marker_Design_2" name="Design primers to features">
3 <description>Design PCR Primers to Features</description>
4 <command interpreter="python">design_primers.py $inputfastaFile $inputSNPfile $inputTargetfile $min_size $max_size > $primer_outputfile </command>
5 <inputs>
6 <param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
7 <param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
8 <param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="Format:Sequence id:source:type:start, such as 1174806:gsMapper:SNP:292" ></param>
9 <param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
10 <param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
11 </inputs>
12 <outputs>
13 <data format="tabular" name="primer_outputfile" />
14 </outputs>
15 <help>
16 .. class:: infomark
17
18 **TIP**
19
20 This tool designs primer pairs to flank features
21
22 It takes
23
24 * an input reference sequence file
25 * a gff3 file containing feature information
26 * a single column file containing list of features
27
28 ----
29
30 **Example**
31
32 --input GFF
33
34 ::
35
36 PGSC0003DMB000000001 samtools SNP 6345 6346 4.84 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6345;Variant_seq=C;Reference_seq=T;Total_reads=2
37 PGSC0003DMB000000001 samtools SNP 6453 6454 18 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6453;Variant_seq=T;Reference_seq=G;Total_reads=8
38 PGSC0003DMB000000001 samtools SNP 7255 7256 149 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7255;Variant_seq=G;Reference_seq=T;Total_reads=14
39 PGSC0003DMB000000001 samtools SNP 7371 7372 86.8 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7371;Variant_seq=C;Reference_seq=T;Total_reads=9
40 PGSC0003DMB000000001 samtools SNP 8288 8289 10.7 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:8288;Variant_seq=A;Reference_seq=G;Total_reads=5
41
42
43 --input features
44
45 ::
46
47 PGSC0003DMB000000001:SAMTOOLS:SNP:1012901
48 PGSC0003DMB000000001:SAMTOOLS:SNP:1021771
49 PGSC0003DMB000000001:SAMTOOLS:SNP:1025761
50 PGSC0003DMB000000001:SAMTOOLS:SNP:1026717
51 PGSC0003DMB000000001:SAMTOOLS:SNP:1026834
52 PGSC0003DMB000000001:SAMTOOLS:SNP:1029542
53
54
55 --output columnar data
56
57 ::
58
59 PGSC0003DMB000000001:SAMTOOLS:SNP:1012901 AGAGGTCGGCTCTCTAGTAGCA GGGGATCCACTAACTATGTCACTT 86
60 PGSC0003DMB000000001:SAMTOOLS:SNP:1021771 CCTATGCGAGAAAGGGACAC GCCCTTCCATGTTGTACGAG 100
61 PGSC0003DMB000000001:SAMTOOLS:SNP:1025761 TGTGAGTAACTTAGTGTCCTACGTCAA CACTCAATGAGCCAAAGCAA 92
62 PGSC0003DMB000000001:SAMTOOLS:SNP:1026717 TTCCTAAGTCATGGGAAAGCA AGTTCATCCAAGGCAAGCAT 76
63 PGSC0003DMB000000001:SAMTOOLS:SNP:1026834 AATGAAGTGACTGGGGAGGA TGCTGGTCGAAGCTTTCTTT 98
64 PGSC0003DMB000000001:SAMTOOLS:SNP:1029542 TAACCAGAAAGTCCGGATGG TTCTGAAGTCAAGTGGGGAGA 75
65
66 -----------------------
67
68 *If you use this tool please cite:*
69
70 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
71 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
72 (2012)
73
74 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
75 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
76
77 </help>
78
79 </tool>