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1 <tool id="snpsplit" name="SNP splitter">
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2
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3 <description>splits multicharacter entries into separate lines</description>
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4
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5 <command interpreter="python">snpsplit.py $input $output</command>
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6
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7 <inputs>
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8
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9 <param name="input" type="data" format="tabular" label="SNP table" />
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10
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11 </inputs>
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12
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13 <outputs>
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14
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15 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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16
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17 </outputs>
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18
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19 <help>
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20
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21
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22 **What it does**
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23
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24
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25
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26 SNPsplit prepares tab-delimited SNP files for TRAMS. It checks each line for entries that contain multiple consecutive bases and splits them over several lines.
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27
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28
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29
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30 - **Input**: tab delimited, format: Position Ref Pol
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31 - Position is 1-based genomic coordinate
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32
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33 - Ref is the reference sequence
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34
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35 - Pol is the polymorphism sequence
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36
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37
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38
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39 Ref en Mut sequences consisting of more than one character will be split up into separate lines. Example:
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40
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41
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42
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43 **Input**:
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44
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45
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46 === === ===
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47
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48 123 CGT ATG
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49
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50 === === ===
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51
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52
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53
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54 **Output**:
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55
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56
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57 === = =
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58
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59 123 C A
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60
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61 124 G T
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62
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63 125 T G
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64
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65 === = =
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66
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67
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68
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69 Bases that are the same in both columns, will be skipped. Example:
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70
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71
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72
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73 **Input**:
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74
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75
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76 === ===== ===
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77
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78 123 C*G*T AGG
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79
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80 === ===== ===
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81
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82
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83
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84 **Output**:
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85
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86
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87 === = =
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88
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89 123 C A
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90
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91 125 T G
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92
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93 === = =
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94
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95
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96 </help>
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97
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98 </tool>
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