Repository revision
7:1dda185ea2d0

Repository 'cutadapt'

Cutadapt tool metadata
Miscellaneous
Cutadapt
Remove adapter sequences from Fastq/Fasta
cutadapt
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/0.9.5.a
0.9.5.a
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.1.a
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/0.9.5.a (this tool)
cutadapt
Requirements (dependencies defined in the <requirements> tag set)
name version type
cutadapt not provided python-module
Additional information about this tool
cutadapt
		#if $input.extension.startswith( "fastq"):
		--format=fastq
		#else
		--format=$input.extension
		#end if 
		#for $a in $adapters
		--adapter='${a.adapter_source.adapter}'
		#end for
		#for $aa in $anywhere_adapters
		--anywhere='${aa.anywhere_adapter_source.anywhere_adapter}'
		#end for
		--error-rate=$error_rate
		--times=$count
		--overlap=$overlap
		#if str($min) != '0':
		--minimum-length=$min
		#end if
		#if str($max) != '0':
		--maximum-length=$max
		#end if
		#if str($quality_cutoff) != '0':
		--quality-cutoff=$quality_cutoff
		#end if
		$discard
		--output='$output' 
		#if str( $output_params.output_type ) == "additional":
			#if $output_params.rest_file:
			--rest-file=$rest_output
			#end if
			#if $output_params.too_short_file:
			--too-short-output=$too_short_output
			#end if
			#if $output_params.untrimmed_file:
			--untrimmed-output=$untrimmed_output
			#end if
		#end if
		'$input'
		> $report
	
None
False
False
Functional tests
name inputs outputs required files
Test-1 input: cutadapt_small.fastq
adapter_source_list: user
adapter:
anywhere_adapter_source_list: user
anywhere_adapter: TTAGACATATCTCCGTCG
output_type: default
output: cutadapt_small.out
cutadapt_small.fastq
cutadapt_small.out
Test-2 input: cutadapt_small.fastq
adapter_source_list: user
adapter: TTAGACATATCTCCGTCG
anywhere_adapter_source_list: user
anywhere_adapter:
discard: true
output_type: default
output: cutadapt_discard.out
cutadapt_small.fastq
cutadapt_discard.out
Test-3 input: cutadapt_rest.fa
adapter_source_list: user
adapter: ADAPTER
anywhere_adapter_source_list: user
anywhere_adapter:
output_type: additional
rest_file: true
output: cutadapt_rest.out
rest_output: cutadapt_rest2.out
cutadapt_rest.fa
cutadapt_rest.out
cutadapt_rest2.out