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find_CAPS.xml
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<?xml version="1.0"?>
<tool id="CAPS_Marker_Design_2" name="CAPS Detection">
<description>identify SNPs that condition restriction polymorphisms</description>
<command interpreter="python">find_CAPS.py $inputFasta $inputSNPGff3File > $outputfile</command>
<inputs>
<param format="gff3" name="inputSNPGff3File" type="data" label="GFF3 file containing SNP data"/>
<param format="fasta" name="inputFasta" type="data" label="fasta source file" />
</inputs>
<outputs>
<data format="interval" name="outputfile" />
</outputs>
<tests>
<test>
<param name="inputSNPGff3File" value="targets.gff" ftype="gff3"/>
<param name="inputFasta" value="targets.fasta" ftype="fasta"/>
<output name="outputfile" file="find_caps_output.txt"/>
</test>
</tests>
<help>
.. class:: infomark
**TIP**
This tool identifies SNPs that condition restriction polymorphisms.
Currently it utilizes a fixed list of robust enzymes known to work well in PCR buffers
AluI,ApaI,BamHI,BbrPI,BfrI,ClaI,DpnI,DraI,EcoRI,HaeIII,HindII,HinfI,HpaI,PvuII,RsaI,SacI,Sau3AI,SmaI,TaqI
It produces a tabular output in interval format
record ID, start, stop, feature ID,enzyme, phase (ie whether it cuts reference or variant sequence)
**Example**
*input GFF3*
::
JR843866 gsmapper SNP 63 63 . . . ID=JR843866:gsmapperSNP:63;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_reads=20
JR843866 gsmapper SNP 146 146 . . . ID=JR843866:gsmapperSNP:146;Reference_seq=T;Variant_seq=C;Total_reads=26;Variant_reads=10
JR843866 gsmapper SNP 258 258 . . . ID=JR843866:gsmapperSNP:258;Reference_seq=T;Variant_seq=G;Total_reads=4;Variant_reads=3
JR848320 gsmapper SNP 157 157 . . . ID=JR848320:gsmapperSNP:157;Reference_seq=C;Variant_seq=T;Total_reads=10;Variant_reads=10
JR848554 gsmapper SNP 54 54 . . . ID=JR848554:gsmapperSNP:54;Reference_seq=T;Variant_seq=G;Total_reads=5;Variant_reads=5
JR848554 gsmapper SNP 74 74 . . . ID=JR848554:gsmapperSNP:74;Reference_seq=C;Variant_seq=T;Total_reads=7;Variant_reads=7
JR848554 gsmapper SNP 123 123 . . . ID=JR848554:gsmapperSNP:123;Reference_seq=T;Variant_seq=A;Total_reads=11;Variant_reads=11
JR848554 gsmapper SNP 147 147 . . . ID=JR848554:gsmapperSNP:147;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_reads=13
JR848554 gsmapper SNP 161 161 . . . ID=JR848554:gsmapperSNP:161;Reference_seq=C;Variant_seq=T;Total_reads=13;Variant_reads=13
*output columnar data*
::
JR843866 63 64 JR843866:gsmapperSNP:63 HaeIII variant
JR848320 157 158 JR848320:gsmapperSNP:157 TaqI variant
JR848320 157 158 JR848320:gsmapperSNP:157 HinfI variant
JR848554 162 163 JR848554:gsmapperSNP:162 TaqI variant
JR848554 162 163 JR848554:gsmapperSNP:162 ClaI variant
JR848554 306 307 JR848554:gsmapperSNP:306 TaqI variant
JR848554 652 653 JR848554:gsmapperSNP:652 TaqI variant
-------------------------------------------------------------------------------
*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>