--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/human_genome_variation/snpFreq.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,104 @@
+<tool id="hgv_snpFreq" name="snpFreq" version="1.0.0">
+  <description>significant SNPs in case-control data</description>
+
+  <command interpreter="perl">
+    snpFreq2.pl $input $group1_1 $group1_2 $group1_3 $group2_1 $group2_2 $group2_3 0.05 $output
+  </command>
+
+  <inputs>
+    <param format="tabular" name="input" type="data" label="Dataset" />
+    <param name="group1_1" label="Column with genotype 1 count for group 1" type="data_column" data_ref="input" />
+    <param name="group1_2" label="Column with genotype 2 count for group 1" type="data_column" data_ref="input" />
+    <param name="group1_3" label="Column with genotype 3 count for group 1" type="data_column" data_ref="input" />
+    <param name="group2_1" label="Column with genotype 1 count for group 2" type="data_column" data_ref="input" />
+    <param name="group2_2" label="Column with genotype 2 count for group 2" type="data_column" data_ref="input" />
+    <param name="group2_3" label="Column with genotype 3 count for group 2" type="data_column" data_ref="input" />
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <requirements>
+    <requirement type="binary">R</requirement>
+  </requirements>
+
+  <tests>
+    <test>
+      <param name="input" ftype="tabular" value="snpFreqInput.txt" dbkey="hg18" />
+      <param name="group1_1" value="4" />
+      <param name="group1_2" value="5" />
+      <param name="group1_3" value="6" />
+      <param name="group2_1" value="7" />
+      <param name="group2_2" value="8" />
+      <param name="group2_3" value="9" />
+      <output name="output" file="snpFreqTestOut.txt" />
+    </test>
+  </tests>
+
+  <help>
+
+**Dataset formats**
+
+The input is tabular_, with six columns of allele counts.  The output is also tabular,
+and includes all of the input data plus the additional columns described below.
+(`Dataset missing?`_)
+
+.. _tabular: ./static/formatHelp.html#tab
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
+**What it does**
+
+This tool performs a basic analysis of bi-allelic SNPs in case-control
+data, using the R statistical environment and Fisher's exact test to
+identify SNPs with a significant difference in the allele frequencies
+between the two groups.  R's "qvalue" package is used to correct for
+multiple testing.
+
+The input file includes counts for each allele combination (AA aa Aa)
+for each group at each SNP position.  The assignment of codes (1 2 3)
+to these genotypes is arbitrary, as long as it is consistent for both
+groups.  Any other input columns are ignored in the computation, but
+are copied to the output.  The output appends eight additional columns,
+namely the minimum expected counts of the three genotypes for each
+group, the p-value, and the q-value.
+
+-----
+
+**Example**
+
+- input file::
+
+    chr1  210  211  38  4  15  56  0   1   x
+    chr1  228  229  55  0  2   56  0   1   x
+    chr1  230  231  46  0  11  55  0   2   x
+    chr1  234  235  43  0  14  55  0   2   x
+    chr1  236  237  55  0  2   13  10  34  x
+    chr1  437  438  55  0  2   46  0   11  x
+    chr1  439  440  56  0  1   55  0   2   x
+    chr1  449  450  56  0  1   13  20  24  x
+    chr1  518  519  56  0  1   38  4   15  x
+
+Here the group 1 genotype counts are in columns 4 - 6, while those
+for group 2 are in columns 7 - 9.
+
+Note that the "x" column has no meaning.  It was added to this example
+to show that extra columns can be included, and to make it easier
+to see where the new columns are appended in the output.
+
+- output file::
+
+    chr1  210  211  38  4  15  56  0   1   x  47    2   8     47    2   8     1.50219088598917e-05  6.32501425679652e-06
+    chr1  228  229  55  0  2   56  0   1   x  55.5  0   1.5   55.5  0   1.5   1                     0.210526315789474
+    chr1  230  231  46  0  11  55  0   2   x  50.5  0   6.5   50.5  0   6.5   0.0155644201009862    0.00409590002657532
+    chr1  234  235  43  0  14  55  0   2   x  49    0   8     49    0   8     0.00210854461554067   0.000739840215979182
+    chr1  236  237  55  0  2   13  10  34  x  34    5   18    34    5   18    6.14613878554783e-17  4.31307984950725e-17
+    chr1  437  438  55  0  2   46  0   11  x  50.5  0   6.5   50.5  0   6.5   0.0155644201009862    0.00409590002657532
+    chr1  439  440  56  0  1   55  0   2   x  55.5  0   1.5   55.5  0   1.5   1                     0.210526315789474
+    chr1  449  450  56  0  1   13  20  24  x  34.5  10  12.5  34.5  10  12.5  2.25757007974134e-18  2.37638955762246e-18
+    chr1  518  519  56  0  1   38  4   15  x  47    2   8     47    2   8     1.50219088598917e-05  6.32501425679652e-06
+
+  </help>
+</tool>