Repository revision

Revision: 71:d96f6c9a39e0

Repository 's_mart'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart

coordinates to sequence tool metadata

Miscellaneous

Name: coordinates to sequence

Description: Coordinates to Sequences: Extract the sequences from a list of coordinates.

Id: coordinatesToSequence

Guid: toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/coordinatesToSequence/1.0.0

Version: 1.0.0

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/coordinatesToSequence/1.0.0 (this tool)

coordinatesToSequence

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

PYTHONPATH

not provided

set_environment

Additional information about this tool

Command:

../Java/Python/coordinatesToSequence.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
			
		-s $sequence
		-o $outputFileFasta

Interpreter: python

Forces a history refresh: False

Functional tests

No functional tests defined