comparison scripts/tools/cg_scripts/Calculate_TestVariants_Variant_Frequencies.xml @ 0:d1920ed3e4fc draft

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0:d1920ed3e4fc

<tool id="pl_calculatefreq" name="Calculate_Variant_Frequencies" version="0.0.1">

  <description>in cgatools-testvariants file</description> <!--adds description in toolbar-->
  
  <command interpreter="perl">
  Calculate_TestVariants_Variant_Frequencies_0_1_0.pl
  --Input $input
  --First_Genome_Field_Nr $first_col
  --Last_Genome_Field_Nr $last_col
  --Output1 $output1
	--Output2 $output2
  </command>

  <outputs>
  	<data format="tabular" name="output1" label="TestVariant_Frequencies on "/>
  	<data format="tabular" name="output2" label="TestVariant_Frequencies_Short on "/>
  </outputs>

  <inputs>
    <param name="input" type="data" format="tabular" label="TestVariants input file">
      <validator type="unspecified_build" />
    </param>
    <param name="first_col" type="text" label="What column number is the first genome"/>
    <param name="last_col" type="text" label="What column number is the last genome"/>
  </inputs>


  <help>

**What it does**

This tool calculates the allele frequencies for all variants present in the testvariant file.

-----

**Instructions**::
	
	Calculate the frequencies of variants in a testvariants output file
	Two values calculated:
		Frequency vs all alleles
		Frequency vs called alleles

	Input: testvariants file
	Outputs:
		All data to *-Freq.tsv, including scores and quals
		vars and freqs to *-Freq_Short.tsv
		Exceptions to *-Freq_Log
		Stats to *-Freq_Stats


	perl Calculate_TestVariants_Variant_Frequencies_0_0_3.pl \
	--Input input_file \
	--First_Genome_Field_Nr col_nr1 \
	--Last_Genome_Field_Nr col_nr2
	--Output1 output1 \
	--Output2 output_short \
	eg
	perl Calculate_TestVariants_Variant_Frequencies_0_0_3.pl \
	--Input /data/Family_Quartet_testvariants.tsv \
	--Output /data/Family_Quartet_testvariants
	--First_Genome_Field_Nr 9 \
	--Last_Genome_Field_Nr 11
	--Output1 /data/Family_Quartet_testvariants
	--Output2 /data/Family_Quartet_testvariants_short
	
  </help>
</tool>