RNBv1.xml

<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>
<process>
    <name>RNB</name>
	<version>1</version>
	<author>
		<name>Fabian Mueller</name>
		<email>fmueller@mpi-inf.mpg.de</email>
	</author>
    <description>
		This process desribes an integrative analysis of bisulfite methylation data. The analysis is run from a configuration JSON file. The input comprises methylation calls in bed format, a comma-separated sample annotation file and options setting in XML format which are specified in the analysis metadata.  The result is a folder structure of multiple HTML reports describing data loading, quality control, site and sample filtering, identification of batch effects, methylation profiling on the basis of indiviual CpGs as well as genomic regions, differential methylation analysis and data export.
		These reports can be viewed locally or displayed via the internet.
	</description>
	<inputs>
		<filetype>
			<identifier>ANALYSIS_CONFIG.JSON</identifier>
			<format></format>
			<quantity>single</quantity>
			<comment>Options settings for RnBeads. These options are also listed in the corresponding analysis metadata.</comment>
		</filetype>
	</inputs>
    <references>
        <filetype>
            <identifier>species_annotation</identifier>
            <format>R package</format>
            <quantity>single</quantity>
            <comment>Assembly specific annotation package containing standard information like CpG islands, promoter regions etc, see http://rnbeads.mpi-inf.mpg.de/installation.php</comment>
        </filetype>
    </references>
	<outputs>
		<filetype>
			<identifier>RNBEADS_REPORT</identifier>
			<format></format>
			<quantity>single</quantity>
			<comment>RnBeads report directory containing HTML reports and associated plots, tables and files.</comment>
		</filetype>
	</outputs>
	<software>
		<tool>
			<name>RnBeads</name>
			<version>>=1.1.3</version>
			<command_line><![CDATA[ Rscript run_rnbeads.R {ANALYSIS_CONFIG.JSON}]]></command_line>
            <loop></loop>
			<comment>Integrated analysis of multiple samples using RnBeads. Pipeline options are transferred to RnBeads via a JSON file, but should also be specified in the anlysis metadata.</comment>
		</tool>
	</software>
</process>