--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pgSnp2gd_snp.xml	Mon Jul 28 11:55:36 2014 -0400
@@ -0,0 +1,97 @@
+<tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0">
+  <description>Convert from pgSnp to gd_snp</description>
+  <command interpreter="perl">
+    #if $snptab.tab2 == "yes" 
+      #if $snptab.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1 
+      #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1
+      #end if
+    #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1
+    #end if
+  </command>
+  <inputs>
+    <param format="tab" name="input1" type="data" label="pgSnp dataset" />
+    <conditional name="snptab">
+      <param name="tab2" type="select" label="Append to gd_snp dataset in history">
+        <option value="yes">yes</option>
+        <option value="no" selected="true">no</option>
+      </param>
+      <when value="yes">
+      <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" />
+        <conditional name="needRef">
+        <param name="colsOnly" type="select" label="Skip new SNPs">
+          <option value="no" selected="true">no</option>
+          <option value="addColsOnly">yes</option>
+        </param>
+        <when value="no"> 
+        <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
+        </when>
+        <when value="addColsOnly"> <!-- do nothing -->
+        </when>
+        </conditional>
+      </when>
+      <when value="no">
+      <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
+      </when>
+    </conditional>
+    <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" />
+  </inputs>
+  <outputs>
+  <data format="gd_snp" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' />
+      <param name='tab2' value='no' />
+      <param name='ref' value='8' />
+      <param name='indName' value='na' />
+      <output name="output" file="pgSnp2snp_output.txt" />
+    </test>
+  </tests>
+
+  <help>
+
+**Dataset formats**
+
+The input dataset is of Galaxy datatype interval_, with the additional columns
+required for pgSnp_ format.
+Any further columns beyond those defined for pgSnp will be ignored.
+The output dataset is a gd_snp_ table.  (`Dataset missing?`_)
+
+.. _interval: ./static/formatHelp.html#interval
+.. _pgSnp: ./static/formatHelp.html#pgSnp
+.. _gd_snp: ./static/formatHelp.html#gd_snp
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
+**What it does**
+
+This tool converts a pgSnp dataset to gd_snp format, either starting a new
+dataset or appending to an old one.  When appending,
+if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or
+backfilled with "-1" (meaning "unknown") for previous individuals/groups in the 
+input gd_snp dataset.
+If any new SNPs are being added (either by creating a new table or by backfilling),
+then an extra column with the reference allele must be supplied in the pgSnp dataset,
+as shown in the example below.
+
+-----
+
+**Example**
+
+- input pgSnp file, with reference allele added::
+
+   chr1    1888681  1888682  C/T     2       4,3     0.8893,0.8453   T
+   chr1    3118325  3118326  T       1       8       0.8796          C
+   chr1    3211457  3211458  A/C     2       17,10   0.8610,0.8576   A
+   etc.
+
+- gd_snp output::
+
+   chr1    1888681   T       C      -1      3       4       1     0.8893
+   chr1    3118325   C       T      -1      0       8       0     0.8796
+   chr1    3211457   A       C      -1      17      10      1     0.8576
+   etc.
+
+</help>
+</tool>