|
4
|
1 <tool id="uniqprimer" name="Uniqprimer" version="0.5.0">
|
|
|
2 <description>Design specific primers of sequences</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="6.6.0">emboss</requirement>
|
|
|
5 <requirement type="package" version="3.23">mummer</requirement>
|
|
|
6 <requirement type="package" version="2.5.0">primer3</requirement>
|
|
6
|
7 <requirement type="package" version="1.70">biopython</requirement>
|
|
4
|
8 </requirements>
|
|
|
9 <command>$__tool_directory__/uniqprimer.sh $include $exclude $product_size_range $primer_size $min_size $max_size $crossvalidate $outfile $log $fasta
|
|
|
10 #for $i in $inputs
|
|
|
11 -i ${i.input}
|
|
|
12 #end for
|
|
|
13
|
|
|
14 </command>
|
|
|
15 <inputs>
|
|
|
16 <param format="fasta" name="include" type="data" label="FASTA file to include" help="Sequences for which you want design specific primer"/>
|
|
|
17 <repeat name="inputs" title="Include FASTA file">
|
|
|
18 <param name="input" label="Add FASTA file to include" type="data" format="fasta" />
|
|
|
19 </repeat>
|
|
|
20 <param format="fasta" name="exclude" type="data" label="FASTA file to exclude" help="Primers will not match these sequences"/>
|
|
|
21 <param type="text" name="product_size_range" label="Product size range" value="100-300"/>
|
|
|
22 <param type="text" name="primer_size" label="Optimal primer size" value="20"/>
|
|
|
23 <param type="text" name="min_size" label="Min primer size" value="18"/>
|
|
|
24 <param type="text" name="max_size" label="Max primer size" value="27"/>
|
|
|
25 <param name="crossvalidate" type="select" label="Cross validate primers against exclude files for extra certainty">
|
|
|
26 <option value="Yes">Yes</option>
|
|
|
27 <option value="No">No</option>
|
|
|
28 </param>
|
|
|
29 </inputs>
|
|
|
30 <outputs>
|
|
|
31 <data format="txt" name="outfile" label="Primer list"/>
|
|
|
32 <data format="fasta" name="fasta" label="Fasta for Primer3"/>
|
|
|
33 <data format="txt" name="log" label="Logfile"/>
|
|
|
34 </outputs>
|
|
|
35 <help>
|
|
|
36
|
|
|
37
|
|
|
38 .. class:: infomark
|
|
|
39
|
|
|
40 **Program encapsulated in Galaxy by IRRI (International Rice Reasearch Institute) and South Green bioinformatics platform**
|
|
|
41
|
|
|
42 .. class:: infomark
|
|
|
43
|
|
|
44 **UniqPrimer version 0.5.0**
|
|
|
45
|
|
|
46 -----
|
|
|
47
|
|
|
48 ==============
|
|
|
49 Please cite:
|
|
|
50 ==============
|
|
|
51
|
|
|
52 "".
|
|
|
53
|
|
|
54 -----
|
|
|
55
|
|
|
56 ===========
|
|
|
57 Overview:
|
|
|
58 ===========
|
|
|
59
|
|
|
60 Uniqprimer designs specific primers of sequences. The goal of this tool is to accept a number of "include" FASTA files of diagnostic target genomes (draft or complete) and "exclude" files of non-target genomes, and output a list of PCR primers that will amplify target genomes but not non-target genomes.
|
|
|
61
|
|
|
62 </help>
|
|
|
63
|
|
|
64 </tool>
|
