Mercurial > repos > john-mccallum > pcr_markers

annotate GVF_Features_Extracter.xml @ 1:a0689dc29b7f draft

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Updated vcf to gff conversion tool
author john-mccallum
date Tue, 31 Jul 2012 00:33:11 -0400
parents 21053f7f9ed1
children
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1 <?xml version="1.0"?>
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2 <tool id="GVF Features Extracter_1" name="GVF Feature ID Extracter">
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3 <description>Extract unique feature IDs from a GVF/GFF3 file </description>
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4 <command >awk '!/^#/ {print $1":"$2":"$3":"$4}' $inputgff3File | sort | uniq > $column_outputfile</command>
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5 <inputs>
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6 <param format="gff3" name="inputgff3File" type="data" label="GVF/Gff3 File"/>
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="column_outputfile" />
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10 </outputs>
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11 <help>
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12
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13 .. class:: infomark
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14
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15 **TIP**
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16
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17 This tool extracts a unique feature identifier from GVF/GFF3 format, primarily to enable downstream analysis of SNPs or marker design
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18
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19
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20 ----
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21
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22 **Example**
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23
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24 *input GFF3*
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25
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26 ::
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27
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28 ##gff-version 3
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29 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
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30 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
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31 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
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32
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33 *output tabular text*
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34
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35 ::
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36
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37 1119927:gsMapper:SNP:434
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38 1120709:gsMapper:SNP:361
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39 1120709:gsMapper:SNP:704
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40
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41 -----------------------------------------------------
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42
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43 *If you use this tool please cite:*
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44
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45 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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46 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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47 (2012)
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48
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49 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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50 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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51
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52 </help>
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53
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54 </tool>