<?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>