Repository revision
71:d96f6c9a39e0

Repository 's_mart'
hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

plot coverage tool metadata
Miscellaneous
Plot the coverage of the first data with respect to the second one.
plotCoverage
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/plotCoverage/1.0.0
1.0.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/plotCoverage/1.0.0 (this tool)
plotCoverage
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/WrappPlotCoverage.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':
			-f gff	
		#elif $formatType.FormatInputFileName1 == 'gff2':
			-f gff2
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'gtf':
			-f gtf
		#end if
			
		-j $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'bed':
			-g bed
		#elif $formatType2.FormatInputFileName2 == 'gff':
			-g gff	
		#elif $formatType2.FormatInputFileName2 == 'gff2':
			-g gff2
		#elif $formatType2.FormatInputFileName2 == 'gff3':
			-g gff3
		#elif $formatType2.FormatInputFileName2 == 'sam':
			-g sam
		#elif $formatType2.FormatInputFileName2 == 'gtf':
			-g gtf
		#end if


		#if $optionRef.Ref == 'Yes':
			-q $optionRef.inputSequenceFile
		#end if

		#if $optionwidth.width == 'Yes':
			-w $optionwidth.widthVal
		#end if
		#if $optionheight.height == 'Yes':
			-e $optionheight.heightVal
		#end if
		#if $optionXlab.Xlab == 'Yes':
			-x $optionXlab.XlabVal
		#end if
		#if $optionYlab.Ylab == 'Yes':
			-y $optionYlab.YlabVal
		#end if
		#if $optiontitle.title == 'Yes':
			-t $optiontitle.titleVal
		#end if	
	
		#if $optionplusColor.plusColor == 'Yes':
			-p $optionplusColor.plusColorVal
		#end if
		#if $optionminusColor.minusColor == 'Yes':
			-m $optionminusColor.minusColorVal
		#end if

		#if $optionsumColor.sumColor == 'Yes':
			-s $optionsumColor.sumColorVal
		#end if
		#if $optionlineColor.lineColor == 'Yes':
			-l $optionlineColor.lineColorVal
		#end if	

		$merge
		-o $outputFile
	
python
False
False
Functional tests
No functional tests defined