comparison SMART/galaxy/getSizes.xml @ 31:0ab839023fe4

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30:5677346472b5

<tool id="GetSizes" name="get sizes">
	<description>Get the sizes of a set of genomic coordinates.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
	
		#if $OptionQuery.OptionQ == 'NONE':
			-q size

		#end if
                #if $OptionY.yLab == "Yes":
		        -b $OptionY.yLabValue
		#end if
		$barPlot
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">

			
			</when>
		</conditional>

		<conditional name="OptionXMax">
			<param name="xMax" type="select" label="maximum x-value to plot">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="maxValue" type="integer" value="1000"/>

			</when>
			<when value="No">
			</when>
		</conditional>

		<param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>
	</inputs>
	
	<outputs>
		<data name="outputFile" format="png" label="[get sizes] output file"/>
	</outputs>

	<help>
Get the sequence/annotation size distribution. A point (*x*, *y*) means that *y* elements have a size of *x* nucleotides. 

When your mapping include exon/intron structures, you can decide to count the size of the introns, the sizes of the exons or the size of the first exons.
	</help>
</tool>

31:0ab839023fe4

<tool id="GetSizes" name="get sizes">
	<description>Get the sizes of a set of genomic coordinates.</description>
	<command interpreter="python">
		../Java/Python/getSizes.py -i $formatType.inputFileName $formatType.FormatInputFileName
	
		#if $OptionQuery.OptionQ == 'NONE':
			-q size

		#end if
                #if $OptionY.yLab == "Yes":
		        -b $OptionY.yLabValue
		#end if
		$barPlot
		$excel $excelOutput
	</command>

	<inputs>
		<conditional name="formatType">
			<param name="FormatInputFileName" type="select" label="Input File Format">

			
			</when>
		</conditional>

		<conditional name="OptionXMax">
			<param name="xMax" type="select" label="maximum value on the x-axis to plot [format: int]">
				<option value="Yes">Yes</option>
				<option value="No" selected="true">No</option>
			</param>
			<when value="Yes">
				<param name="maxValue" type="integer" value="1000"/>

			</when>
			<when value="No">
			</when>
		</conditional>



		<param name="barPlot" type="boolean" truevalue="-B" falsevalue="" checked="false" label="use barplot representation"/>

		<param name="excel" type="boolean" truevalue="-c" falsevalue="" checked="false" label="excel option" help="This option creates a csv file."/>
	</inputs>
	
	<outputs>
		<data name="outputFile" format="png" label="[Get sizes] output file"/>
		<data name="excelOutput" format="csv">
			<filter>excel</filter>
		</data>
	</outputs>
</tool>