<tool id="chr_prefix" name="Add/Remove chr prefix" version="1">

  <description> add or remove chr prefix from a column </description>
  
   <code file="getcolumnnames.py"/>
   
  <command interpreter="bash"> 
  	chrprefix.sh 
  		$infile
  		"${go.column}"
  		$addremove
		$outputfile		
  </command>

  <outputs>
  	<data format="tabular" name="outputfile" label="${sample} - chr-prefix on ${on_string}"/>
  </outputs>
  
  <inputs>

  	<param name="infile" type="data" label="Select inputfile" help="must be a tab-delimited file with a 1-line header" />   
  	<conditional name="go">
		<param name="ready" type="select"  label="Ready to select column?"  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">		
  			<param name="column"   type="select" dynamic_options="get_headers(infile)"  multiple="False" label="Select Column"   />
  		</when>
  	</conditional>		
  		
  	<param name="addremove" type="select" label="Add or remove the chr prefix?">
  		<option value="add">Add</option>
  		<option value="remove">Remove</option> 
  	</param> 
  	<param name="sample"	type="text" value="" label="Output File Name" help="Optional."/>	

  </inputs>

  <help>
  
**What it does**
removes or adds the "chr" prefix in a column of a file. Some tools expect you to indicate chromosomes as "chr1,chr2,chrX", while others expect only 1,2,X as input. This tool allows you to easily switch notations

  </help>
</tool>