Mercurial > repos > john-mccallum > pcr_markers
diff GVF_Features_Extracter.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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GVF_Features_Extracter.xml Thu Jun 14 19:29:26 2012 -0400 @@ -0,0 +1,54 @@ +<?xml version="1.0"?> +<tool id="GVF Features Extracter_1" name="GVF Feature ID Extracter"> + <description>Extract unique feature IDs from a GVF/GFF3 file </description> + <command >awk '!/^#/ {print $1":"$2":"$3":"$4}' $inputgff3File | sort | uniq > $column_outputfile</command> + <inputs> + <param format="gff3" name="inputgff3File" type="data" label="GVF/Gff3 File"/> + </inputs> + <outputs> + <data format="tabular" name="column_outputfile" /> + </outputs> +<help> + +.. class:: infomark + +**TIP** + +This tool extracts a unique feature identifier from GVF/GFF3 format, primarily to enable downstream analysis of SNPs or marker design + + +---- + +**Example** + +*input GFF3* + +:: + + ##gff-version 3 + 1119927 gsMapper SNP 434 434 . . . ID=1119927:gsMapper:SNP:434;Reference_seq=G;Variant_seq=A;Total_reads=10;Variant_freq=100;Enzyme=AluI;Phase=variant + 1120709 gsMapper SNP 361 361 . . . ID=1120709:gsMapper:SNP:361;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_freq=68;Enzyme=TaqI;Phase=variant + 1120709 gsMapper SNP 704 704 . . . ID=1120709:gsMapper:SNP:704;Reference_seq=A;Variant_seq=G;Total_reads=20;Variant_freq=90;Enzyme=RsaI;Phase=variant + +*output tabular text* + +:: + + 1119927:gsMapper:SNP:434 + 1120709:gsMapper:SNP:361 + 1120709:gsMapper:SNP:704 + + ----------------------------------------------------- + +*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>