comparison xcms_datatypes/README.txt @ 0:d00379767dbf draft default tip

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README
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   XCMS Suite datatypes: A Workflow for metabolomics by ABIMS team
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This package contains the datatypes for the XCMS suite.

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Instructions for integration of the XCMS datatypes into the workflow-system
Galaxy (http://getgalaxy.org)
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In order to install the datatypes for the XCMS Suite into your Galaxy installation, please do the following:

$galaxybase: Your galaxy-dist location

-- Add the two datatypes and sniffer to the $galaxybase/datatypes_conf.xml

        <datatype extension="ms_zip" type="galaxy.datatypes.xcms:MSZip" display_in_upload="true" />
		<datatype extension="rdata" type="galaxy.datatypes.xcms:RData" display_in_upload="true" />
		<sniffer type="galaxy.datatypes.xcms:MSZip"/>

-- Copy xcms.py to $galaxybase/lib/galaxy/datatypes/

-- Add "import xcms" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py

-- Modify the $galaxybase/tools/data_source/upload.py:


	-At the beginning of the file, put this line :
		from galaxy.datatypes.xcms import *
	-Then add the function:
		def check_ms_zip( file_name ):
		return MSZip().sniff( file_name )
	-Add the following lines between the two <ABIMS insert lines> :
	
	if image:
			if not PIL:
				image = None
			# get_image_ext() returns None if nor a supported Image type
			ext = get_image_ext( dataset.path, image )
			data_type = ext
		# Is dataset content multi-byte?
		elif dataset.is_multi_byte:
			data_type = 'multi-byte char'
		ext = sniff.guess_ext( dataset.path, is_multi_byte=True )
		# <Abims insert Lines>
		# Is dataset content supported Abims datatype
		elif check_ms_zip( dataset.name ):
			ext = 'ms_zip'
			data_type = 'ms_zip'
		# </Abims insert lines >
		# Is dataset content supported sniffable binary?



Last but not least, restart Galaxy.