<tool id="CleanTranscriptFile" name="clean transcript file">
	<description>Clean a transcript file so that it is useable for S-MART.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName 
		#if $formatType.FormatInputFileName == 'gff':
		 	-f gff
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#end if	
		#if $optionType.type == 'Yes':
			-t $optionType.value
		#end if 
		-o $outputFile 
	</command> 

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName"  type="select" label="Input File Format">
				<option value="gff">gff</option>
				<option value="gtf">gtf</option>
				<option value="gff3">gff3</option>
			 </param>
			 <when value="gff">
				 <param name="inputFileName" format="gff" type="data" label="Input File"/>	 
			</when>
			<when value="gtf"> 
			         <param name="inputFileName" format="gtf" type="data" label="Input File"/> 
			 </when>
			<when value="gff3"> 
			         <param name="inputFileName" format="gff3" type="data" label="Input File"/> 
			 </when>
		 </conditional>
 
		 <conditional name="optionType">

		<param name="type" type="select" label="You can choose the tag that you are interested in, like tRNA,rRNA,ncRNA,CDS,exon, etc." help="Name of the types you want to keep in GFF/GTF (list separated by commas)">
			<option value="Yes">Yes</option>
			<option value="No" selected="true">No</option>
		</param>
		<when value="Yes">
			 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/>
		</when>
		<when value="No">
		</when>
	</conditional>

	</inputs>


	<outputs>
		<data name="outputFile" format="gtf">
			<change_format>
			<when input="formatType.FormatInputFileName" value="gtf" format="gtf" />
			<when input="formatType.FormatInputFileName" value="gff" format="gff" />
			<when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
		</change_format> 
		</data>

	</outputs>
<tests>
    <test>
      <param name="FormatInputFileName" value="gtf" />
      <param name="inputFileName" value="genes.gtf" />
      <param name="type" value="No" />
      <output name="outputFile" file="exp_cleantranscriptfile_genes.gtf" />
    </test>
  </tests>

	<help>
		A GFF/GTF file (please consult http://www.sequenceontology.org/gff3.shtml to know more about the GFF3 format, and http://mblab.wustl.edu/GTF22.html for the GTF format) may contain different sources of information: chromosome size, genes, transcripts, etc. S-MART mostly works on transcripts. This scripts filters the input file to keep the information you really want, based on the feature (3rd column).
	</help>

</tool>