Repository revision
71:d96f6c9a39e0

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

mapper analyzer tool metadata
Miscellaneous
Read the output of an aligner, print statistics and possibly translate into GFF, BED or GBrowse formats.
mapperAnalyzer
toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/mapperAnalyzer/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/mapperAnalyzer/1.0.0 (this tool)
mapperAnalyzer
Requirements (dependencies defined in the <requirements> tag set)
name version type
PYTHONPATH not provided set_environment
Additional information about this tool
../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff3':
			-f gff3	
		#elif $formatType.FormatInputFileName1 == 'sam':
			-f sam
		#elif $formatType.FormatInputFileName1 == 'bam':
			-f bam
		#elif $formatType.FormatInputFileName1 == 'seqmap':
			-f seqmap
		#end if
			
		-q $formatType2.inputFileName2
		#if $formatType2.FormatInputFileName2 == 'fasta':
			-k fasta
		#elif $formatType2.FormatInputFileName2 == 'fastq':
			-k fastq	
		#end if
		

		#if $optionnumber.number == 'Yes':
			-n $optionnumber.numberVal
		#end if
		#if $optionsize.size == 'Yes':
			-s $optionsize.sizeVal
		#end if
		#if $optionidentity.identity == 'Yes':
			-d $optionidentity.identityVal
		#end if
		#if $optionmismatch.mismatch == 'Yes':
			-m $optionmismatch.mismatchVal
		#end if
		#if $optiongap.gap == 'Yes':
			-p $optiongap.gapVal
		#end if		
		#if $optiontitle.title == 'Yes':
			-t $optiontitle.titleVal
		#end if	
		#if $optionappend.append == 'Yes':
			-a $optionappend.appendfile
		#end if	
			
		$merge
		$remove
		$remain
		-o $outputFileGFF
	
python
False
False
Functional tests
No functional tests defined