--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/get_flanks.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,78 @@
+<tool id="get_flanks1" name="Get flanks">
+  <description>returns flanking region/s for every gene</description>
+  <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
+  <inputs>
+    <param format="interval" name="input" type="data" label="Select data"/>
+    <param name="region" type="select" label="Region">
+      <option value="whole" selected="true">Whole feature</option>
+      <option value="start">Around Start</option>
+      <option value="end">Around End</option>
+    </param>
+    <param name="direction" type="select" label="Location of the flanking region/s">
+      <option value="Upstream">Upstream</option>
+      <option value="Downstream">Downstream</option>
+      <option value="Both">Both</option>
+    </param>
+    <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
+    <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
+    
+    
+  </inputs>
+  <outputs>
+    <data format="interval" name="out_file1" metadata_source="input"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="flanks_inp.bed"/>
+      <param name="offset" value="-500"/>
+      <param name="size" value="1000"/>
+      <param name="direction" value="Both"/>
+      <param name="region" value="whole"/>
+      <output name="out_file1" file="flanks_out1.bed"/>
+    </test>
+    <test>
+      <param name="input" value="flanks_inp.bed"/>
+      <param name="offset" value="200"/>
+      <param name="size" value="1000"/>
+      <param name="direction" value="Downstream"/>
+      <param name="region" value="start" />
+      <output name="out_file1" file="flanks_out2.bed"/>
+    </test>
+  </tests>
+ <help> 
+
+This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 
+
+**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
+
+-----
+
+
+**Example 1**
+
+- For the following query::
+
+   chr22  1000  7000  NM_174568 0 +
+
+- running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
+
+   chr22  500  800  NM_174568 0 +
+
+.. image:: ./static/operation_icons/flanks_ex1.gif
+
+**Example 2**
+
+- For the following query::
+
+   chr22  1000  7000  NM_028946 0 -
+
+- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
+
+   chr22  500  800  NM_028946 0 -
+
+.. image:: ./static/operation_icons/flanks_ex2.gif
+
+</help>  
+
+
+</tool>
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