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

Uploaded

30:5677346472b5

<tool id="coordinatesToSequence" name="coordinates to sequence">
	<description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
	<requirements>
		<requirement type="set_environment">PYTHONPATH</requirement>
	</requirements>
	<command interpreter="python">
		../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':

	<outputs>
		<data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
	</outputs> 
	
	<help>
You can use this tool, if you just want to convert your mapping data to genomic coordinates, without any filtering. It requires a genomic coordinates file together with its format, an output format (GFF3, BED, etc...), the genome, and prints you the corresponding file.
	</help>
</tool>

31:0ab839023fe4

<tool id="coordinatesToSequence" name="coordinates to sequence">
	<description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
	<command interpreter="python">
		../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
		#if $formatType.FormatInputFileName1 == 'bed':
			-f bed
		#elif $formatType.FormatInputFileName1 == 'gff':

	<outputs>
		<data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
	</outputs> 
	
</tool>