view smart_toolShed/SMART/galaxy/getNb.xml @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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<tool id="getNumber" name="get number">
	<description>Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster.</description>
	<command interpreter="python">
		../Java/Python/ -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
		#elif $formatType.FormatInputFileName == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName == 'gtf':
			-f gtf
		#end if
		-o $outputFilePNG
		-q $query
		#if $optionXMAX.XMAX == 'Yes':
			-x $optionXMAX.xMaxValue
		#end if		


		<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>
				<option value="sam">sam</option>
				<option value="gtf">gtf</option>
			<when value="bed">
				<param name="inputFileName" format="bed" type="data" label="Input File"/>
			<when value="gff">
				<param name="inputFileName" format="gff" type="data" label="Input File"/>
			<when value="gff2">
				<param name="inputFileName" format="gff2" type="data" label="Input File"/>
			<when value="gff3">
				<param name="inputFileName" format="gff3" type="data" label="Input File"/>
			<when value="sam">
				<param name="inputFileName" format="sam" type="data" label="Input File"/>
			<when value="gtf">
				<param name="inputFileName" format="gtf" type="data" label="Input File"/>
		<param name="query" type="text" value="None" label="compulsory option, choice (exon, transcript, cluster)" />
		<param name="barPlot" type="boolean" truevalue="-b" falsevalue="" checked="false" label="use barplot representation"/>
		<conditional name="optionXMAX">
			<param name="XMAX" type="select" label="maximum value on the x-axis to plot ">
					<option value="Yes">Yes</option>
					<option value="No" selected="true">No</option>
			<when value="Yes">
				<param name="xMaxValue" type="integer" value="0" />
			<when value="No">

		<data name="outputFilePNG" format="png" label="[getNB]out file"/>