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1 <?xml version="1.0"?>
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2 <tool id="gsMapper_to_gff3_1" name="Convert gsMapper to gff3">
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3 <description>Convert Roche gsMapper to GFF3</description>
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4 <command interpreter="bash">gsmapper2gff.sh $inputGsFile $outputfile</command>
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5 <inputs>
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6 <param format="txt" name="inputGsFile" type="data" label="Roche gsMapper 454HCDiffs.txt or 454AllDiffs.txt file"/>
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7
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8 </inputs>
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9 <outputs>
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10 <data format="gff3" name="outputfile" />
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11 </outputs>
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12 <help>
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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 parses Roche gsMapper read mapping output into GVF/GFF3 format
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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*
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25
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26 ::
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27
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28 >Reference Start End Ref Var Total Var Ref Var Coding Region Known # Fwd # Rev # Fwd # Rev
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29 >Accno Pos Pos Nuc Nuc Depth Freq AA AA Frame Name SNP's w/ var w/ var Total Total
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30 ______________________________
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31
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32 >1118212 673 673 A C 7 100% 6 1 6 1
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33
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34 Reads with Difference:
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35 1118212 648+ GTTGGTCCACTATTACTCTCAGATT-ATTTCATAACAATAATGG----A-TAC-AA 696
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36 **
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37 FX289JP01DVQR7 53- GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGGGCTGA-TACTA 1
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38 FX289JP02IJT2O (7) 82+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 130
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39 FX289JP01B8R7V 84+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATA-TGG----A-TAC-AA 131
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40 FX289JP02FX58L 68+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----AC-AC-AA 116
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41 FX289JP02JXAX7 (7) 67+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 115
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42 FX289JP02JOOQZ (2) 69+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 117
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43 FX289JP02GPHPX 45+ GTTGGTCCACTATTACTCTCAGATTC-TTTCATAACAATAATGG----A-TAC-AA 93
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44 **
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45
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46
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47 *output*
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48
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49 ::
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50
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51 ##gff-version 3
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52 1118212 gsMapper SNP 673 673 . . . ID=1118212:gsMapper:SNP:673;Reference_seq=A;Variant_seq=C;Total_reads=7;Variant_freq=100;
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53 1118212 gsMapper SNP 730 730 . . . ID=1118212:gsMapper:SNP:730;Reference_seq=A;Variant_seq=G;Total_reads=13;Variant_freq=31;
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54 1118212 gsMapper SNP 782 782 . . . ID=1118212:gsMapper:SNP:782;Reference_seq=T;Variant_seq=C;Total_reads=13;Variant_freq=92;
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55 1118212 gsMapper SNP 1319 1319 . . . ID=1118212:gsMapper:SNP:1319;Reference_seq=G;Variant_seq=A;Total_reads=7;Variant_freq=100;
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56
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57 -----------------------
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58
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59 *If you use this tool please cite:*
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60
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61 A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data:
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62 Application For Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
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63 (2012)
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64
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65 Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright,
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66 Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum
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67
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68
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69 </help>
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70 </tool>
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