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1 <tool id="vcf2pgSnp" name="VCF to pgSnp" hidden="false" version="1.0.0">
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2 <description>Convert from VCF to pgSnp format</description>
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3 <command interpreter="perl">
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4 #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1
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5 #else #vcf2pgSnp.pl $inType.ind_column $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="vcf" name="input1" type="data" label="VCF dataset" />
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10 <conditional name="inType">
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11 <param name="how" type="select" label="How to treat individuals">
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12 <option value="all">Group all as a population</option>
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13 <option value="one">Do just one individual</option>
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14 </param>
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15 <when value="one">
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16 <param name="ind_column" type="data_column" data_ref="input1" label="Column to convert" value="10" />
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17 </when>
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18 <when value="all">
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19 <!-- do nothing -->
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20 </when>
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21 </conditional>
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22 </inputs>
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23 <outputs>
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24 <data format="interval" name="out_file1" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input1" value="vcf2pgSnp_input.vcf" ftype="vcf" />
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29 <param name="how" value="all" />
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30 <output name="output" file="vcf2pgSnp_output.pgSnp" />
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31 </test>
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32 </tests>
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33
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34 <help>
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35 **Dataset formats**
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36
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37 The input dataset is VCF_ format.
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38 The output dataset is pgSnp_. (`Dataset missing?`_)
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39
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40 .. _Dataset missing?: ./static/formatHelp.html
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41 .. _VCF: ./static/formatHelp.html#vcf
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42 .. _pgSnp: ./static/formatHelp.html#pgSnp
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43
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44 -----
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45
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46 **What it does**
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47
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48 This converts a VCF dataset to pgSnp with the frequency counts being
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49 chromosome counts. If there is more than one column of SNP data it will either
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50 accumulate all columns as a population or convert the column indicated
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51 to pgSnp.
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52
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53 -----
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54
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55 **Examples**
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56
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57 - input::
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58
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59 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48
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60 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48
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61 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48
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62 etc.
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63
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64 - output as a population::
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65
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66 chr1 13326 13327 G/C 2 7,1 0,0
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67 chr1 13979 13980 T/C 2 7,1 0,0
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68 chr1 30922 30923 G/T 2 4,4 0,0
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69 etc.
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70
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71 - output for each column separately::
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72
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73 chr1 13326 13327 G 1 2 0 G/C 2 1,1 0,0 G 1 2 0 G 1 2 0
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74 chr1 13979 13980 T 1 2 0 T/C 2 1,1 0,0 T 1 2 0 T 1 2 0
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75 chr1 30922 30923 T 1 2 0 G 1 2 0 G 1 2 0 T 1 2 0
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76 etc.
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77
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78 </help>
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79 </tool>
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