--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/column_extract.xml	Thu Oct 22 09:18:30 2015 -0400
@@ -0,0 +1,50 @@
+<tool id="column_select" name="Column Select" version="1">
+
+  <description> extract/rearrange columns from a tab-delimited file </description>
+  <code file="getcolumnnames.py"/>
+
+  <command interpreter="bash"> 
+  	column_extract.sh 
+		$infile
+		$outputfile
+		$removeheader
+		#for $c in $go.columns
+			${c.column}
+		#end for
+  </command>
+
+  <outputs>
+  	<data format="tabular" name="outputfile" label="${sample} Column extract on ${on_string}"/>
+  </outputs>
+  
+  <inputs>
+
+   <param name="infile" type="data" label="Select file to extract columns from" help="Must be a tab-separated file with a 1-line header"/>   	
+   <param name="removeheader" type="boolean" truevalue="Y" falsevalue="N" selected="false" label="Remove header?" help="If selected, any lines starting with # and any empty lines will not be output."/>
+   
+   <conditional name="go">
+		<param name="ready" type="select"  label="Ready to select columns?"  help="Set to NO and back to YES after changing input file">
+			<option value="no" selected="True">no</option>
+			<option value="yes">yes</option>	
+		</param>
+			
+		<when value="yes">		
+		   <repeat name="columns" title="Column" min="1">
+		   		<!-- <param name="col"     type="data_column"   data_ref="infile" multiple="False" label="Column from file to output"  /> -->
+				<param name="column"   type="select" dynamic_options="get_headers(infile)"  multiple="False" label="Select Column"   />
+		   </repeat>	
+	   	</when>
+   </conditional>
+   
+  <param name="sample"	type="text" value="" label="Sample Name" help="Optional. For file naming purposes only"/>	
+
+  </inputs>
+
+  <help>
+  
+
+**What it does**
+Outputs columns of input file in order specified by user. Columns not selected will not be output. 
+
+  </help>
+</tool>