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design_primers.xml
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<?xml version="1.0"?>
<tool id="Genetic_Marker_Design_2" name="Design primers to features">
<description>Design PCR Primers to Features</description>
<command interpreter="python -W ignore">
#if 'Yes' in $uMelt.value
design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size -u > $primer_outputfile
#else
design_primers.py -i $inputfastaFile -g $inputSNPfile -T $inputTargetfile -p $min_size -P $max_size > $primer_outputfile
#end if
</command>
<inputs>
<param format="fasta" name="inputfastaFile" type="data" label="Multifasta Source file" />
<param format="gff3" name="inputSNPfile" type="data" label="annotation file(Gff3)" />
<param format="txt" name="inputTargetfile" type="data" optional="false" label="Target file" help="IN FORMAT Sequence id:source:type:start e.g. 1174806:gsMapper:SNP:292" ></param>
<param name="min_size" size="20" type="text" value="75" label="Minimum Product Size Range" />
<param name="max_size" size="20" type="text" value="100" label="Maximum Product Size Range" />
<param name="uMelt" type="select" label="uMelt prediction for HRM">
<option value="No" selected= "true">No</option>
<option value="Yes">Yes</option>
</param>
</inputs>
<outputs>
<data format="tabular" name="primer_outputfile" />
</outputs>
<stdio>
<exit_code range="1:" level="fatal" description="Fatal Error" />
</stdio>
<help>
.. class:: infomark
**TIP**
This tool designs primer pairs to flank features
Optionally it can predict reference and variant Tm using the uMelt web service provided by University of Utah
It takes
* an input reference sequence file
* a gff3 file containing feature information
* a single column file containing list of features
----
**Example**
--input GFF
::
PGSC0003DMB000000001 samtools SNP 6345 6346 4.84 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6345;Variant_seq=C;Reference_seq=T;Total_reads=2
PGSC0003DMB000000001 samtools SNP 6453 6454 18 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:6453;Variant_seq=T;Reference_seq=G;Total_reads=8
PGSC0003DMB000000001 samtools SNP 7255 7256 149 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7255;Variant_seq=G;Reference_seq=T;Total_reads=14
PGSC0003DMB000000001 samtools SNP 7371 7372 86.8 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:7371;Variant_seq=C;Reference_seq=T;Total_reads=9
PGSC0003DMB000000001 samtools SNP 8288 8289 10.7 . . ID=PGSC0003DMB000000001:SAMTOOLS:SNP:8288;Variant_seq=A;Reference_seq=G;Total_reads=5
--input features
::
PGSC0003DMB000000001:SAMTOOLS:SNP:1012901
PGSC0003DMB000000001:SAMTOOLS:SNP:1021771
PGSC0003DMB000000001:SAMTOOLS:SNP:1025761
PGSC0003DMB000000001:SAMTOOLS:SNP:1026717
PGSC0003DMB000000001:SAMTOOLS:SNP:1026834
PGSC0003DMB000000001:SAMTOOLS:SNP:1029542
--output columnar data
::
PGSC0003DMB000000001:SAMTOOLS:SNP:1012901 AGAGGTCGGCTCTCTAGTAGCA GGGGATCCACTAACTATGTCACTT 86
PGSC0003DMB000000001:SAMTOOLS:SNP:1021771 CCTATGCGAGAAAGGGACAC GCCCTTCCATGTTGTACGAG 100
PGSC0003DMB000000001:SAMTOOLS:SNP:1025761 TGTGAGTAACTTAGTGTCCTACGTCAA CACTCAATGAGCCAAAGCAA 92
PGSC0003DMB000000001:SAMTOOLS:SNP:1026717 TTCCTAAGTCATGGGAAAGCA AGTTCATCCAAGGCAAGCAT 76
PGSC0003DMB000000001:SAMTOOLS:SNP:1026834 AATGAAGTGACTGGGGAGGA TGCTGGTCGAAGCTTTCTTT 98
PGSC0003DMB000000001:SAMTOOLS:SNP:1029542 TAACCAGAAAGTCCGGATGG TTCTGAAGTCAAGTGGGGAGA 75
-----------------------
*If you use this tool please cite:*
A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)
Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
</help>
</tool>