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comparison uniqprimer.xml @ 4:1306b28be7c3 draft

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author dereeper
date Mon, 03 Jan 2022 10:06:48 +0000
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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>
7 </requirements>
8 <command>$__tool_directory__/uniqprimer.sh $include $exclude $product_size_range $primer_size $min_size $max_size $crossvalidate $outfile $log $fasta
9 #for $i in $inputs
10 -i ${i.input}
11 #end for
12
13 </command>
14 <inputs>
15 <param format="fasta" name="include" type="data" label="FASTA file to include" help="Sequences for which you want design specific primer"/>
16 <repeat name="inputs" title="Include FASTA file">
17 <param name="input" label="Add FASTA file to include" type="data" format="fasta" />
18 </repeat>
19 <param format="fasta" name="exclude" type="data" label="FASTA file to exclude" help="Primers will not match these sequences"/>
20 <param type="text" name="product_size_range" label="Product size range" value="100-300"/>
21 <param type="text" name="primer_size" label="Optimal primer size" value="20"/>
22 <param type="text" name="min_size" label="Min primer size" value="18"/>
23 <param type="text" name="max_size" label="Max primer size" value="27"/>
24 <param name="crossvalidate" type="select" label="Cross validate primers against exclude files for extra certainty">
25 <option value="Yes">Yes</option>
26 <option value="No">No</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data format="txt" name="outfile" label="Primer list"/>
31 <data format="fasta" name="fasta" label="Fasta for Primer3"/>
32 <data format="txt" name="log" label="Logfile"/>
33 </outputs>
34 <help>
35
36
37 .. class:: infomark
38
39 **Program encapsulated in Galaxy by IRRI (International Rice Reasearch Institute) and South Green bioinformatics platform**
40
41 .. class:: infomark
42
43 **UniqPrimer version 0.5.0**
44
45 -----
46
47 ==============
48 Please cite:
49 ==============
50
51 "".
52
53 -----
54
55 ===========
56 Overview:
57 ===========
58
59 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.
60
61 </help>
62
63 </tool>