# HG changeset patch
# User bcrain-completegenomics
# Date 1337886921 14400
# Node ID fec197eb2f00ecb2db7bc269635a08abbb0292c8
# Parent  8caa26b33983adcb0314a89feb51d75db957c0b2
Uploaded

diff -r 8caa26b33983 -r fec197eb2f00 Calculate_TestVariants_Variant_Frequencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Calculate_TestVariants_Variant_Frequencies.xml	Thu May 24 15:15:21 2012 -0400
@@ -0,0 +1,67 @@
+<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>