--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpsplit.xml	Fri Apr 05 05:00:40 2013 -0400
@@ -0,0 +1,98 @@
+<tool id="snpsplit" name="SNP splitter">
+
+  <description>splits multicharacter entries into separate lines</description>
+
+  <command interpreter="python">snpsplit.py $input $output</command>
+
+  <inputs>
+
+    <param name="input" type="data" format="tabular" label="SNP table" />
+
+  </inputs>
+
+  <outputs>
+
+    <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
+
+  </outputs>
+
+  <help>
+
+
+**What it does**
+
+
+
+SNPsplit prepares tab-delimited SNP files for TRAMS. It checks each line for entries that contain multiple consecutive bases and splits them over several lines.
+
+
+
+- **Input**: tab delimited, format: Position Ref Pol
+- Position is 1-based genomic coordinate
+
+- Ref is the reference sequence
+
+- Pol is the polymorphism sequence
+
+
+
+Ref en Mut sequences consisting of more than one character will be split up into separate lines. Example:
+
+
+
+**Input**:
+
+
+=== === ===
+
+123 CGT ATG
+
+=== === ===
+
+
+
+**Output**:
+
+
+=== = =
+
+123 C A
+
+124 G T
+
+125 T G
+
+=== = =
+
+
+
+Bases that are the same in both columns, will be skipped. Example:
+
+
+
+**Input**:
+
+
+=== ===== ===
+
+123 C*G*T AGG
+
+=== ===== ===
+
+
+
+**Output**:
+
+
+=== = =
+
+123 C A
+
+125 T G
+
+=== = =
+
+
+  </help>
+
+</tool>