# HG changeset patch
# User devteam
# Date 1377006064 14400
# Node ID e342ab27851f44ab4fdb823b9e4932ecf996cc61
# Parent  137ec95c8ca6f3a1a70fddd3ce7496b327217851
Uploaded tool tarball without .bak file.

diff -r 137ec95c8ca6 -r e342ab27851f dividePgSnpAlleles.xml.bak
--- a/dividePgSnpAlleles.xml.bak	Tue Aug 20 09:39:35 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<tool id="dividePgSnp" name="Separate pgSnp alleles" hidden="false">
-  <description>into columns</description>
-  <command interpreter="perl">
-    #if $refcol.ref == "yes" #dividePgSnpAlleles.pl -ref=$refcol.ref_column $input1 > $out_file1
-    #else #dividePgSnpAlleles.pl $input1 > $out_file1
-    #end if
-  </command>
-  <inputs>
-    <param format="interval" name="input1" type="data" label="pgSnp dataset" />
-    <conditional name="refcol">
-      <param name="ref" type="select" label="Dataset has a column with the reference allele:">
-        <option value="yes">yes</option>
-        <option value="no" selected="true">no</option>
-      </param>
-      <when value="yes">
-      <param name="ref_column" type="data_column" data_ref="input1" label="Column with reference allele" />
-      </when>
-      <when value="no"> <!-- do nothing -->
-      </when>
-    </conditional>
-  </inputs>
-  <outputs>
-  <data format="interval" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name='input1' value='dividePgSnp_input.pgSnp' ftype='interval' />
-      <param name='ref' value='no' />
-      <output name="output" file="dividePgSnp_output.txt" />
-    </test>
-  </tests>
-
-  <help>
-**Dataset formats**
-
-The input dataset is of Galaxy datatype interval_ with the columns specified
-for pgSnp_.
-Any additional columns beyond the pgSnp defined columns will be appended to
-the output.
-The output dataset is in interval_ format.  (`Dataset missing?`_)
-
-.. _interval: ./static/formatHelp.html#interval
-.. _Dataset missing?: ./static/formatHelp.html
-.. _pgSnp: ./static/formatHelp.html#pgSnp
-
-**What it does**
-
-This separates the alleles from a pgSnp dataset into separate columns,
-as well as the frequencies and scores that go with the alleles.  It will skip
-any positions with more than 2 alleles.  If only a single allele is given then "N"
-will be used for the second, with a frequency and score of zero.  Or, if a 
-column with reference alleles is provided, 
-the value in that column will be used in place of the "N" for single alleles.
-
------
-
-**Examples**
-
-- input pgSnp file::
-
-   chr1    256     257     A/C     2       3,4     10,20
-   chr1    56100   56101   A       1       5       30
-   chr1    77052   77053   A/G     2       6,7     40,50
-   chr1    110904  110905  A       1       8       60
-   etc.
-
-- output::
-
-   chr1    256     257     A       3       10       C       4       20
-   chr1    56100   56101   A       5       30       N       0       0
-   chr1    77052   77053   A       6       40       G       7       50
-   chr1    110904  110905  A       8       60       N       0       0
-   etc.
-
-</help>
-</tool>