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1 <tool id="dividePgSnp" name="Separate pgSnp alleles" hidden="false">
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2 <description>into columns</description>
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3 <command interpreter="perl">
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4 #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1
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5 #else #dividePgSnpAlleles.pl $input1 > $out_file1
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6 #end if
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7 </command>
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8 <inputs>
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9 <param format="interval" name="input1" type="data" label="pgSnp dataset" />
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10 <conditional name="refcol">
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11 <param name="ref" type="select" label="Dataset has a column with the reference allele:">
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12 <option value="yes">yes</option>
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13 <option value="no" selected="true">no</option>
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14 </param>
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15 <when value="yes">
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16 <param name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" />
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17 </when>
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18 <when value="no"> <!-- do nothing -->
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19 </when>
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20 </conditional>
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21 </inputs>
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22 <outputs>
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23 <data format="interval" name="out_file1" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' />
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28 <param name='ref' value='no' />
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29 <output name="output" file="dividePgSnp_output.txt" />
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30 </test>
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31 </tests>
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32
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33 <help>
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34 **Dataset formats**
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35
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36 The input dataset is of Galaxy datatype interval_ with the columns specified
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37 for pgSnp_.
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38 Any additional columns beyond the pgSnp defined columns will be appended to
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39 the output.
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40 The output dataset is in interval_ format. (`Dataset missing?`_)
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41
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42 .. _interval: ./static/formatHelp.html#interval
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43 .. _Dataset missing?: ./static/formatHelp.html
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44 .. _pgSnp: ./static/formatHelp.html#pgSnp
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45
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46 **What it does**
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47
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48 This separates the alleles from a pgSnp dataset into separate columns,
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49 as well as the frequencies and scores that go with the alleles. It will skip
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50 any positions with more than 2 alleles. If only a single allele is given then "N"
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51 will be used for the second, with a frequency and score of zero. Or, if a
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52 column with reference alleles is provided,
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53 the value in that column will be used in place of the "N" for single alleles.
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54
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55 -----
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56
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57 **Examples**
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58
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59 - input pgSnp file::
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60
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61 chr1 256 257 A/C 2 3,4 10,20
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62 chr1 56100 56101 A 1 5 30
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63 chr1 77052 77053 A/G 2 6,7 40,50
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64 chr1 110904 110905 A 1 8 60
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65 etc.
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66
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67 - output::
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68
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69 chr1 256 257 A 3 10 C 4 20
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70 chr1 56100 56101 A 5 30 N 0 0
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71 chr1 77052 77053 A 6 40 G 7 50
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72 chr1 110904 110905 A 8 60 N 0 0
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73 etc.
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74
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75 </help>
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76 </tool>
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