annotate column_extract.xml @ 0:e77c9484b2d0 draft default tip

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<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>