Mercurial > repos > john-mccallum > pcr_markers
comparison design_primers.xml @ 0:21053f7f9ed1 draft
First upload of PCR Marker tools
author | john-mccallum |
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date | Thu, 14 Jun 2012 19:29:26 -0400 |
parents | |
children | a0689dc29b7f |
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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> |