CHPv0.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>CHP</name>
	<version>0</version>
	<author>
		<name>Peter Ebert</name>
		<email>pebert@mpi-inf.mpg.de</email>
	</author>
    <description>
		ANDREAS: please insert general comments here
	</description>
	<inputs>
		<filetype>
			<identifier>ALNv0_histone.bam</identifier>
			<format></format>
			<quantity>collection</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>ALNv0_input.bam</identifier>
			<format></format>
			<quantity>single</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>ALNv0.bai</identifier>
			<format></format>
			<quantity>collection</quantity>
			<comment>Index files are renamed internally to .bam.bai since deepTools is expecting index naming like this</comment>
		</filetype>
	</inputs>
	<references>
		<filetype>
			<identifier>ref_genome</identifier>
			<format>2bit</format>
			<quantity>single</quantity>
			<comment>The reference genome file</comment>
		</filetype>
		<filetype>
			<identifier>chip_ctrl_regions</identifier>
			<format>BED</format>
			<quantity>single</quantity>
			<comment>Control regions obtained from Freiburg for quality control of ChIPseq samples</comment>
		</filetype>
	</references>
	<outputs>
		<filetype>
			<identifier>samplesID.PROCESS.DATE.corplot.png</identifier>
			<format>deepTools graphics PNG</format>
			<quantity>single</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>samplesID.PROCESS.DATE.fgprplot.png</identifier>
			<format>deepTools graphics PNG</format>
			<quantity>single</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>sampleID.PROCESS.DATE.gcbplot.png</identifier>
			<format>deepTools graphics PNG</format>
			<quantity>collection</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>sampleID.PROCESS.DATE.gcbfreq.txt</identifier>
			<format></format>
			<quantity>collection</quantity>
			<comment></comment>
		</filetype>
		<filetype>
			<identifier>sampleIDs.PROCESS.DATE.bamcomp.bw</identifier>
			<format></format>
			<quantity>collection</quantity>
			<comment></comment>
		</filetype>
	</outputs>
	<software>
		<tool>
			<name>bamCorrelate (deepTools)</name>
			<version>1.5.1-252-gbbb0711</version>
			<command_line><![CDATA[ bamCorrelate bins -p {numproc} --bamfiles {ALNv0_histone.bam} {ALNv0_input.bam} --labels {labels} --plotFile {samplesID.PROCESS.DATE.corplot.png} --fragmentLength {fragment_length} --corMethod {correlation_method} ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>bamFingerprint (deepTools)</name>
			<version>1.5.1-252-gbbb0711</version>
			<command_line><![CDATA[ bamFingerprint {numproc} {bamfiles} --labels {labels} --plotFile {samplesID.PROCESS.DATE.fgprplot.png} --fragmentLength {fragment_length} ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>computeGCBias (deepTools)</name>
			<version>1.5.1-252-gbbb0711</version>
			<command_line><![CDATA[ computeGCBias -p {numproc} --bamfile {ALNv0_*.bam} --effectiveGenomeSize {genomesize} --genome {reference_genome} --GCbiasFrequenciesFile {sampleID.PROCESS.DATE.gcbfreq.txt} --biasPlot {sampleID.PROCESS.DATE.gcbplot.png} ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>MACS2</name>
			<version>macs2 2.0.10.20130915 (tag:beta)</version>
			<command_line><![CDATA[ macs2 callpeak -f BAM {bamfile} {control} --gsize {genomesize} {outname} --keep-dup all --nomodel --extsize 200 --qvalue 0.01 ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>bamCompare (deepTools)</name>
			<version>1.5.1-252-gbbb0711</version>
			<command_line><![CDATA[ bamCompare {numproc} {bamfile1} {bamfile2} --outFileName sampleIDs.PROCESS.DATE.bamcomp.bw --outFileFormat bigwig --fragmentLength 200 --scaleFactorsMethod SES ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>bamCoverage (deepTools)</name>
			<version>1.5.1-252-gbbb0711</version>
			<command_line><![CDATA[ bamCoverage {numproc} {bamfile} --outFileName sampleID.PROCESS.DATE.bamcov.bw --outFileFormat bigwig --fragmentLength 200 ]]></command_line>
            <loop>no looping</loop>
			<comment></comment>
		</tool>
	</software>
</process>