<module name="ngs">

	<category name="Quality control" color="#d5c796">
		<tool runtime="R-2.12">
			<resource>fastqc.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>fastx-statistics.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-statistics.R</resource>
		</tool>
	</category>
	
	<category name="Filtering" color="#e7df70">
		<tool runtime="R-2.12">
			<resource>fastx-quality-filter.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>prinseq-length-filter.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-N-filter.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-complexity-filter.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-duplicate-filter.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-filter.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>fastx-clipper.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-filter-annotations.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-filter-results-column.R</resource>
		</tool>
	</category>

	<category name="Utilities" color="#d59f45">
		<tool runtime="R-2.12">
			<resource>ngs-create-experiment.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>tagcleaner-predict.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>tagcleaner-statistics.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>tagcleaner-trim.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>fastx-trimmer.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-quality-trimmer.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-AT-trimmer.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>prinseq-trimmer.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>fastx-renamer.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-rmdup.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-index.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-sort-index-BAM.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-convert-SAMtoBAM-sort-index.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-bamtobed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>fastx-fastq-to-fasta.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-merge.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-idxstats.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>subset-fastq.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-subset.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-count.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>samtools-consensus.R</resource>
		</tool>
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.SortBed</resource>
		</tool>
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.SortGtf</resource>
		</tool>
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.SortVcf</resource>
		</tool>		
		<tool runtime="R-2.12">
			<resource>bedtools-slopbed.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>extract-features-from-BED.R</resource>
		</tool>		
	    <tool runtime="R-2.12">
			<resource>test-data-in.R</resource>
		</tool>	
        <tool runtime="R-2.12">
			<resource>test-data-in-out.R</resource>
		</tool>	
	</category>

	<category name="Matching sets of genomic regions" color="#e7881c">
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.regions.FindOverlappingTool
			</resource>
		</tool>
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.regions.RemoveOverlappingTool
			</resource>
		</tool>
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.regions.CombineRegionsTool
			</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-subtractbed.R</resource>
		</tool>	
		<tool runtime="R-2.12">
			<resource>bedtools-intersectbed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-closestbed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-windowbed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-mergebed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-coveragebed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-genomecoveragebed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-overlap.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-pairtobed.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bedtools-pairtopair.R</resource>
		</tool>	
	</category>

	<category name="Alignment" color="#d53833">
		<tool runtime="R-2.12">
			<resource>bowtie2.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie2-paired-end.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie2-with-index-building.R</resource>
		</tool>
	    <tool runtime="R-2.12">
			<resource>bowtie2-paired-end-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>tophat2.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>tophat2-single-end.R</resource>
		</tool>
	    <tool runtime="R-2.12">
			<resource>bwa.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bwa-paired-end.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bwa-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bwa-paired-end-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bwasw-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie-paired-end.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>bowtie-paired-end-with-index-building.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>tophat.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>tophat-single-end.R</resource>
		</tool>
	</category>
	
	<category name="Variants" color="#80a3b7">
		<tool runtime="R-2.12">
			<resource>samtools-snp-indel-single.R</resource>
		</tool> 
		<tool runtime="R-2.12">
			<resource>vcftools.R</resource>
		</tool>
		<tool runtime="R-2.15_bioc-2.11">
			<resource>annotate-variant.R</resource>
		</tool>
	</category>
	
	<category name="RNA-seq" color="#0177b7">
		<tool runtime="R-2.12">
			<resource>htseq-count.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>htseq-count-own-gtf.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>dexseq-exoncount.R</resource>
		</tool>
		<tool runtime="R-2.14">
			<resource>dea-deseq.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-dea-edger-RNA.R</resource>
		</tool>
		<tool runtime="R-2.15">
			<resource>edgeR-multivariate.R</resource>
		</tool>
		<tool runtime="R-2.15">
			<resource>DEXseq.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>cufflinks2.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>cuffmerge2.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>cuffdiff2.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>dea-cufflinks.R</resource>
		</tool>
		<tool runtime="beanshell" module="common">
			<resource>annotate-cpdb.bsh</resource>
		</tool>
	</category>

	<category name="miRNA-seq" color="#629a9b">
		<tool runtime="R-2.12">
			<resource>convert-bam-to-edger.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>convert-miRBase-bam-to-edger.R</resource>
		</tool>
		<!--
		<tool runtime="java">
			<resource>fi.csc.chipster.tools.ngs.regions.FindOverlappingDatabaseTool</resource>
		</tool>
		-->
		<tool runtime="R-2.12">
			<resource>ngs-dea-edger.R</resource>
		</tool>
		<tool runtime="R-2.14">
			<resource>dea-deseq.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-annotate-miRNA-targets.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-pathways-mirna-hyperg-go.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-pathways-mirna-hyperg-kegg.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-correlation-analysis-mirna.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-up-down-analysis-mirna.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-extract-target-gene-expression.R</resource>
		</tool>
	</category>

	<category name="ChIP-seq and FAIRE-seq" color="#c0d2de">
		<tool runtime="R-2.12">
			<resource>ngs-find-peaks-macs-one.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-find-peaks-macs-two.R</resource>
		</tool>		
		<tool runtime="R-2.12">
			<resource>ngs-find-motifs-jaspar.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-find-nearest-genes.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-find-unique-genes.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>pathways-ngs-hyperg-go.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>ngs-find-peaks-fseq.R</resource>
		</tool>
	</category>

	<!--<category name="FAIRE-seq and DNAse-seq" color="#66CCFF">
		<tool runtime="R-2.12">
			<resource>ngs-find-peaks-fseq.R</resource>
		</tool>
		
		<tool runtime="R-2.15">
			<resource>ngs-find-peaks-zinba.R</resource>
		</tool>
		
	</category>-->

	<category name="CNA-seq" color="#a49900">
		<tool runtime="R-2.15_bioc-2.11"><resource>cna-bin-hits.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>cna-define-experiment.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>cna-correct.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-normalize.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-profile.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11"><resource>cna-segment.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-call-aberrations.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-identify-regions.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-frequencies.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-cluster.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-group-test.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-survival-test.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-survival.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-convert-from-probes-to-genes.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-pathways-go.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-match-probes.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-combined-profile.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-expression-test.R</resource></tool>	
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-plot-combined-expression.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-add-cytobands.R</resource></tool>
		<tool runtime="R-2.15_bioc-2.11" module="common"><resource>acgh-count-overlapping-cnvs.R</resource></tool>
	</category>

	<category name="Methyl-seq" color="#83010b">
		<tool runtime="R-2.12">
			<resource>convertBAMtoMEDIPS.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>combineMEDIPS.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>MEDIPS_one_sample.R</resource>
		</tool>
		<tool runtime="R-2.12">
			<resource>MEDIPS_two_samples.R</resource>
		</tool>
	</category>
</module>
