view SMART/galaxy/changeTagName.xml @ 6:769e306b7933

Change the repository level.

<tool id="changeTagName" name="change tag name">
	<description>Changes the name of tag of a list of transcripts.</description>
	<command interpreter="python">
		../Java/Python/changeTagName.py -i $formatType.inputFileName
		#if $formatType.FormatInputFileName == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName == 'gff':
			-f gff
		#elif $formatType.FormatInputFileName == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName == 'gff3':
			-f gff3
		#end if

		-t $Tag
		-n $name
			
		-o $outputFileGff 
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">
				<option value="bed">bed</option>
				<option value="gff">gff</option>
				<option value="gff2">gff2</option>
				<option value="gff3">gff3</option>
			</param>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			</when>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			</when>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			</when>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			</when>
		</conditional>

		<param name="Tag" type="text" value="None" label="tag option" help="A given tag, you must choose a tag."/>
		<param name="name" type="text" value="None" label="name option" help="new name for the tag, you must choose a new name."/>		
	
		

	</inputs>

	<outputs>
		<data name="outputFileGff" format="gff3" label="[changeTagName] Output File"/>
	</outputs> 
	
</tool>