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1 <tool id="pl_calculatefreq" name="Calculate_Variant_Frequencies" version="0.0.1">
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2
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3 <description>in cgatools-testvariants file</description> <!--adds description in toolbar-->
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4
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5 <command interpreter="perl">
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6 Calculate_TestVariants_Variant_Frequencies_0_1_0.pl
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7 --Input $input
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8 --First_Genome_Field_Nr $first_col
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9 --Last_Genome_Field_Nr $last_col
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10 --Output1 $output1
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11 --Output2 $output2
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12 </command>
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13
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14 <outputs>
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15 <data format="tabular" name="output1" label="TestVariant_Frequencies on "/>
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16 <data format="tabular" name="output2" label="TestVariant_Frequencies_Short on "/>
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17 </outputs>
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18
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19 <inputs>
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20 <param name="input" type="data" format="tabular" label="TestVariants input file">
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21 <validator type="unspecified_build" />
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22 </param>
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23 <param name="first_col" type="text" label="What column number is the first genome"/>
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24 <param name="last_col" type="text" label="What column number is the last genome"/>
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25 </inputs>
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26
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27
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28 <help>
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29
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30 **What it does**
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31
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32 This tool calculates the allele frequencies for all variants present in the testvariant file.
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33
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34 -----
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35
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36 **Instructions**::
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37
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38 Calculate the frequencies of variants in a testvariants output file
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39 Two values calculated:
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40 Frequency vs all alleles
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41 Frequency vs called alleles
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42
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43 Input: testvariants file
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44 Outputs:
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45 All data to *-Freq.tsv, including scores and quals
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46 vars and freqs to *-Freq_Short.tsv
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47 Exceptions to *-Freq_Log
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48 Stats to *-Freq_Stats
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49
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50
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51 perl Calculate_TestVariants_Variant_Frequencies_0_0_3.pl \
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52 --Input input_file \
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53 --First_Genome_Field_Nr col_nr1 \
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54 --Last_Genome_Field_Nr col_nr2
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55 --Output1 output1 \
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56 --Output2 output_short \
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57 eg
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58 perl Calculate_TestVariants_Variant_Frequencies_0_0_3.pl \
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59 --Input /data/Family_Quartet_testvariants.tsv \
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60 --Output /data/Family_Quartet_testvariants
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61 --First_Genome_Field_Nr 9 \
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62 --Last_Genome_Field_Nr 11
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63 --Output1 /data/Family_Quartet_testvariants
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64 --Output2 /data/Family_Quartet_testvariants_short
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65
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66 </help>
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67 </tool>
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