EXPv1.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>EXP</name>
	<version>1</version>
	<author>
		<name>Matthias Barann</name>
		<email>m.barann@ikmb.uni-kiel.de</email>
	</author>
    <description>
		* bam2wig.py: Conversion of BAM file to BigWig coverage tracks. One track per strand will be generated.
		* htseq-count: Generates read counts on the gene level.
		* cufflinks: Generates FPKM values for genes and transcript isoforms.
	</description>
	<inputs>
		<filetype>
			<identifier>.bam</identifier>
			<format></format>
			<quantity>single</quantity>
			<comment>Unfiltered aligned reads</comment>
		</filetype>
		<filetype>
			<identifier>.bai</identifier>
			<format></format>
			<quantity>single</quantity>
			<comment>Index file to bam file</comment>
		</filetype>
	</inputs>
	<references>
		<filetype>
			<identifier>chromInfo.txt</identifier>
			<format>text file</format>
			<quantity>single</quantity>
			<comment>Tab delimited file containing the name and length of the reference sequences: [name][tab][length].</comment>
		</filetype>
		<filetype>
			<identifier>gencode.v19.annotation.gtf</identifier>
			<format>GTF</format>
			<quantity>single</quantity>
			<comment>Gencode gene annotation file in gene transfer format.</comment>
		</filetype>
		<filetype>
			<identifier>reference.fa</identifier>
			<format>multi fasta</format>
			<quantity>single</quantity>
			<comment>The reference genome file; see aspera.dkfz.de > download > results > references > genomes > human > WholeGenome</comment>
		</filetype>
	</references>
	<outputs>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].bamcov.Forward.wig</identifier>
			<format>wiggle</format>
			<quantity>single</quantity>
			<comment>Forward strand wiggle file. Usually it is not necessary to keep this file.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].bamcov.Reverse.wig</identifier>
			<format>wiggle</format>
			<quantity>single</quantity>
			<comment>Reverse strand wiggle file Usually it is not necessary to keep this file.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].bamcov.Forward.bw</identifier>
			<format>BigWig</format>
			<quantity>single</quantity>
			<comment>Forward strand BigWig file. This file will only be generated if the UCSC program bamToBigWig can be found in $PATH.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].bamcov.Reverse.bw</identifier>
			<format>BigWig</format>
			<quantity>single</quantity>
			<comment>Reverse strand BigWig file. This file will only be generated if the UCSC program bamToBigWig can be found in $PATH.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].readcounts.txt</identifier>
			<format>text file</format>
			<quantity>single</quantity>
			<comment>This file contains the read counts on the gene level.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].genes.fpkm.tracking</identifier>
			<format>text file</format>
			<quantity>single</quantity>
			<comment>Output file containing the FPKM counts on the gene level.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].isoforms.fpkm.tracking</identifier>
			<format>text file</format>
			<quantity>single</quantity>
			<comment>Output file containing the FPKM counts on the isoform level.</comment>
		</filetype>
		<filetype>
			<identifier>[sampleID].EXPv1.[DATE].transcripts.gtf</identifier>
			<format>gene transfer format</format>
			<quantity>single</quantity>
			<comment>This file contains assembled transcripts.</comment>
		</filetype>
	</outputs>
	<software>
		<tool>
			<name>Python</name>
			<version>2.7</version>
			<command_line><![CDATA[ CMDLINE ]]></command_line>
			<loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>Samtools</name>
			<version>0.1.19-44428cd</version>
			<command_line><![CDATA[ CMDLINE ]]></command_line>
			<loop>no looping</loop>
			<comment></comment>
		</tool>
		<tool>
			<name>bam2wig.py</name>
			<version>2.3.9</version>		
			<command_line><![CDATA[ python bam2wig.py -i ${sample}.bam -s ChromInfo.txt -o ${_sample} -d "1+-,1-+,2++,2--" ]]></command_line>
            <loop>no looping</loop>
			<comment>The python script is part of the RSeQC software. It will convert a bam file into two wig files (one for each strand). \
			If the UCSC program wigToBigWig can be located by the python script, the generated wig files will automatically be converted to bigWig. \
			Please note that for some samples the wigToBigWig command might exit with errors. In this case, manually invoking the wigToBigWig \
			command on the generated wig files can solve the problem: \
			wigToBigWig ${_sample}_Forward.wig -s ChromInfo.txt > ${_sample}_Forward.bw</comment>
		</tool>
		<tool>
			<name>htseq-count</name>
			<version>0.5.4p3</version>		
			<command_line><![CDATA[ samtools sort -n -@ 8 -m 4G ${_sample}.bam ${_sample}_sorted
			samtools/samtools view -F 256 ${_sample}_sorted.bam > ${_sample}.sam
			htseq-count -s reverse  -m intersection-strict -a 20 ${_sample}.sam gencode.v19.annotation.gtf > ${_sample}_htseq.txt ]]>
			</command_line>
            <loop>no looping</loop>
			<comment>DESeq requires bam files sorted by read name (step 1). After sorting, all non-primary alignments are removed during the bam to sam conversion. \
			Invoking htseq-count counts the number of reads per gene. Using the mode 'intersection-strict' results in a rather conservative read count. \
			Please see http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count for further information.</comment>
		</tool>
		<tool>
			<name>cufflinks</name>
			<version>v2.0.2</version>		
			<command_line><![CDATA[ cufflinks -p 8 --frag-bias-correct reference.fa --multi-read-correct --library-type fr-firststrand --compatible-hits-norm -G gencode.v19.annotation_transcripts_only.gtf ${_sample}.bam ]]>
			</command_line>
            <loop>no looping</loop>
			<comment>Please see http://cufflinks.cbcb.umd.edu/manual.html for further information.</comment>
		</tool>
	</software>
</process>