# HG changeset patch # User bgruening # Date 1391686805 18000 # Node ID 2ad3b027dfcd251800e343338dfa9102f931bcd0 # Parent d2898b81b912c873774fcc3145bb1054369a8b7f Uploaded diff -r d2898b81b912 -r 2ad3b027dfcd Galaxy-Workflow-1_BAM_file_--_(clustered)_Heatmap_of_read_coverages.ga --- a/Galaxy-Workflow-1_BAM_file_--_(clustered)_Heatmap_of_read_coverages.ga Tue Feb 04 13:45:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,262 +0,0 @@ -{ - "a_galaxy_workflow": "true", - "annotation": "1 BAM file from D.melanogaster will be normalized to 1x sequencing depth and a heatmap can be generated for a user-specified BED file (with genes being scaled to a length of 1.5kb)", - "format-version": "0.1", - "name": "1 BAM file -->(clustered) Heatmap of read coverages", - "steps": { - "0": { - "annotation": "sorted BAM file, e.g. Input from Data Library", - "id": 0, - "input_connections": {}, - "inputs": [ - { - "description": "sorted BAM file, e.g. Input from Data Library", - "name": "file of mapped reads" - 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"tool_version": "1.0.3", - "type": "tool", - "user_outputs": [] - } - } -} \ No newline at end of file diff -r d2898b81b912 -r 2ad3b027dfcd bamCompare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCompare.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,220 @@ + + normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig) + + + + bamCompare + deepTools_macros.xml + + + bamCompare + + @THREADS@ + + --bamfile1 '$bamFile1' + -bai1 '${bamFile1.metadata.bam_index}' + --bamfile2 '$bamFile2' + -bai2 '${bamFile2.metadata.bam_index}' + + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' + + --fragmentLength $fragmentLength + --binSize $binSize + + #if $scaling.method == 'SES': + --scaleFactorsMethod SES + --sampleLength $scaling.sampleLength + #elif $scaling.method == 'readCount': + --scaleFactorsMethod readCount + #elif $scaling.method == 'own': + --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2' + #end if + + --ratio $comparison.type + + #if $comparison.type=='subtract': + #if $comparison.normalization.type=='rpkm': + --normalizeUsingRPKM + #elif $comparison.normalization.type=='1x': + + #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize + #else: + --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt + #end if + + #end if + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.smoothLength: + --smoothLength '$advancedOpt.smoothLength' + #end if + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates + + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + + --missingDataAsZero $advancedOpt.missingDataAsZero + + #if str($advancedOpt.ignoreForNormalization).strip() != '': + --ignoreForNormalization $advancedOpt.ignoreForNormalization + #end if + + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool compares two BAM files based on the number of mapped reads. To +compare the BAM files, the genome is partitioned into bins of equal size, +the reads are counted for each bin and each BAM file and finally, a summarizing value is reported. +This value can be the ratio of the number of reads per bin, the log2 of the ratio or the difference. +This tool can normalize the number of reads on each BAM file using the SES method +proposed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). Normalization based on read counts is also available. The +output is either a bedGraph or a bigWig file containing the bin location and +the resulting comparison values. +If paired-end reads are present, the fragment +length reported in the BAM file is used by default. + + +.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png + + +You can find more details on the bamCompare wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare + + +**Output files**: + +- same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files. + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd bamCorrelate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCorrelate.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,167 @@ + + correlates pairs of BAM files + + + + bamCorrelate + deepTools_macros.xml + + + #set files=[] + #set labels=[] + + @multiple_input_bams@ + + bamCorrelate + + $mode.modeOpt + + @THREADS@ + + --bamfiles #echo " ".join($files) + --labels #echo " ".join($labels) + --fragmentLength $fragmentLength + --corMethod $corMethod + + --plotFile $outFileName + + #if $output.showOutputSettings == "yes" + --outRawCounts '$outFileRawCounts' + --outFileCorMatrix '$outFileCorMatrix' + --plotFileFormat $output.outFileFormat + #else: + --plotFileFormat 'png' + #end if + + #if $mode.modeOpt == "bins": + --binSize '$mode.binSize' + --numberOfSamples '$mode.numberOfSamples' + #else: + --BED $mode.region_file + #end if + + #### options available in both modes + #if str($mode.region.value) != '': + --region '$mode.region' + #end if + + #if $mode.advancedOpt.showAdvancedOpt == "yes": + + $mode.advancedOpt.doNotExtendPairedEnds + $mode.advancedOpt.ignoreDuplicates + $mode.advancedOpt.includeZeros + + #if $mode.advancedOpt.minMappingQuality: + --minMappingQuality '$mode.advancedOpt.minMappingQuality' + #end if + + #if $mode.advancedOpt.zMin: + --zMin $mode.advancedOpt.zMin + #end if + #if $mode.advancedOpt.zMax: + --zMax $mode.advancedOpt.zMax + #end if + --colorMap '$mode.advancedOpt.colorMap' + + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveRawCounts'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveCorMatrix'] is True + )) + + + + + +**What it does** + +This tool is useful to assess the overall similarity of different BAM files. A typical application +is to check the correlation between replicates or published data sets. + +The tool splits the genomes into bins of given length. For each bin, the number of reads +found in each BAM file is counted and a correlation (either Pearson or Spearman) is computed for all +pairs of BAM files. Finally, a heatmap is drawn based on the similarity of the samples. + + +.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png + :alt: Heatmap of RNA Polymerase II ChIP-seq + + +You can find more details on the bamCorrelate wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamCorrelate + + +**Output files**: + +- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation, see below for an example +- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used + + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd bamCoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCoverage.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,157 @@ + + generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig) + + + + bamCoverage + deepTools_macros.xml + + + bamCoverage + + @THREADS@ + + --bam '$bamInput' + --bamIndex ${bamInput.metadata.bam_index} + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' + + --fragmentLength $fragmentLength + --binSize $binSize + + #if $scaling.type=='rpkm': + --normalizeUsingRPKM + #elif $scaling.type=='1x': + #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize + #else: + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt + #end if + #elif $scaling.type=='own': + --scaleFactor $scaling.scaleFactor + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.smoothLength: + --smoothLength '$advancedOpt.smoothLength' + #end if + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates + + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + + ##if str($advancedOpt.ignoreForNormalization).strip() != '': + ## --ignoreForNormalization $advancedOpt.ignoreForNormalization + ##end if + + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Given a BAM file, this tool generates a bigWig or bedGraph file with genome-wide coverage of fragment or read coverages. +The way the method works is by first calculating all the number of reads (either extended to match the fragment length or not) +that overlap each bin (a region of fixed length, i.e. 25 bp) in the genome. Bins with zero counts are skipped, i.e. not added to the output file. +The resulting read counts can be normalized using either a given scaling factor, the RPKM formula or to get a 1x depth of coverage (RPGC). + + +.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png + + +You can find more details on the bamCoverage wiki page: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage + + +**Output files**: + +- coverage file either in bigWig or bedGraph format + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd bamFingerprint.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamFingerprint.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,151 @@ + + plots profiles of BAM files; useful for assesing ChIP signal strength + + + + bamFingerprint + deepTools_macros.xml + + + @multiple_input_bams@ + + bamFingerprint + + @THREADS@ + + --bamfiles #echo " ".join($files) + --labels #echo " ".join($labels) + + --fragmentLength $fragmentLength + + #set newoutFileName=str($outFileName)+".png" + --plotFile $newoutFileName + + #if $output.showOutputSettings == "yes" + --plotFileFormat $output.outFileFormat + #if $output.saveRawCounts: + --outRawCounts '$outFileRawCounts' + #end if + #else + --plotFileFormat 'png' + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + --binSize '$advancedOpt.binSize' + --numberOfSamples '$advancedOpt.numberOfSamples' + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates + $advancedOpt.skipZeros + + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + #end if + ; mv $newoutFileName $outFileName + ; rm $temp_dir -rf + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveRawCounts'] is True + )) + + + + + +**What it does** + +This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal) +and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3). + +The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length. +These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank) +and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads +along the genome (i.e. without enrichments in open chromatin etc.) should +generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep +rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in +few bins which corresponds to high, narrow enrichments seen for transcription factors. + + +.. image:: $PATH_TO_IMAGES/QC_fingerprint.png + + +You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint + + +**Output files**: + +- Diagnostic plot +- Data matrix of raw counts + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd computeGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeGCBias.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,155 @@ + + to see whether your samples should be normalized for GC bias + + + + computeGCBias + deepTools_macros.xml + + + ln -s $bamInput local_bamInput.bam; + ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; + + computeGCBias + @THREADS@ + + --bamfile 'local_bamInput.bam' + --GCbiasFrequenciesFile $outFileName + --fragmentLength $fragmentLength + + @reference_genome_source@ + + #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize + #else: + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + + --sampleSize '$advancedOpt.sampleSize' + --regionSize '$advancedOpt.regionSize' + + #if $advancedOpt.filterOut: + --filterOut $advancedOpt.filterOut + #end if + + #if $advancedOpt.extraSampling: + --extraSampling $advancedOpt.extraSampling + #end if + #end if + + #if str($image_format) != 'none': + --biasPlot $outImageName + --plotFileFormat $image_format + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + image_format != 'none' + )) + + + + + + + + + + + +**What it does** + +This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations) +The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. +There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot +depicting the ratio of observed/expected reads per genomic GC content bin. + +----- + +**Summary of the method used** + +In order to estimate how many reads with what kind of GC content one should have sequenced, we first need to determine how many regions the specific +reference genome contains for each amount of GC content, i.e. how many regions in the genome have 50% GC (or 10% GC or 90% GC or...). +We then sample a large number of equally sized genome bins and count how many times we see a bin with 50% GC (or 10% GC or 90% or...). These EXPECTED values are independent of any +sequencing as it only depends on the respective reference genome (i.e. it will most likely vary between mouse and fruit fly due to their genome's different GC contents). +The OBSERVED values are based on the reads from the sequenced sample. Instead of noting how many genomic regions there are per GC content, we now count the reads per GC content. +In an ideal sample without GC bias, the ratio of OBSERVED/EXPECTED values should be close to 1 regardless of the GC content. Due to PCR (over)amplifications, the majority of ChIP samples +usually shows a significant bias towards reads with high GC content (>50%) + +.. image:: $PATH_TO_IMAGES/QC_GCplots_input.png + + +You can find more details on the computeGCBias wiki page: computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias + + +**Output files**: + +- Diagnostic plot + + - box plot of absolute read numbers per genomic GC bin + - x-y plot of observed/expected read ratios per genomic GC content bin + +- Data matrix + + - to be used for GC correction with correctGCbias + + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd computeMatrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrix.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,222 @@ + + summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile + + + + computeMatrix + deepTools_macros.xml + + + #import tempfile + + #set $temp_input_handle = tempfile.NamedTemporaryFile() + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + + #for $rf in $regionsFiles: + cat "$rf.regionsFile" >> $temp_input_path; + #if str($rf.label.value).strip(): + echo "\#$rf.label.value" >> $temp_input_path; + #else: + echo "\#$rf.regionsFile.name" >> $temp_input_path; + #end if + #end for + + + computeMatrix + + $mode.mode_select + --regionsFileName '$temp_input_path' + --scoreFileName '$scoreFile' + --outFileName '$outFileName' + + @THREADS@ + + #if $output.showOutputSettings == "yes" + #if $output.saveData: + --outFileNameData '$outFileNameData' + #end if + #if $output.saveMatrix: + --outFileNameMatrix '$outFileNameMatrix' + #end if + + #if $output.saveSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #end if + + #if $mode.mode_select == "reference-point": + --referencePoint $mode.referencePoint + $mode.nanAfterEnd + --beforeRegionStartLength $mode.beforeRegionStartLength + --afterRegionStartLength $mode.afterRegionStartLength + #else + --regionBodyLength $mode.regionBodyLength + --startLabel "$mode.startLabel" + --endLabel "$mode.endLabel" + #if $mode.regionStartLength.regionStartLength_select == "yes": + --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength + --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength + #end if + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + --sortRegions '$advancedOpt.sortRegions' + --sortUsing '$advancedOpt.sortUsing' + --averageTypeBins '$advancedOpt.averageTypeBins' + $advancedOpt.missingDataAsZero + $advancedOpt.skipZeros + --binSize $advancedOpt.binSize + + #if $advancedOpt.minThreshold: + --minThreshold $advancedOpt.minThreshold + #end if + #if $advancedOpt.maxThreshold: + --maxThreshold $advancedOpt.maxThreshold + #end if + #if $advancedOpt.scale: + --scale $advancedOpt.scale + #end if + + #end if + ; rm $temp_input_path + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool prepares an intermediary file (a gzipped table of values) +that contains scores associated with genomic regions that can be used +afterwards to plot a heatmap or a profile. + +Genomic regions can really be anything - genes, parts of genes, ChIP-seq +peaks, favorite genome regions... as long as you provide a proper file +in BED or INTERVAL format. If you would like to compare different groups of regions +(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group. + +computeMatrix can also be used to filter and sort +regions according to their score by making use of its advanced output options. + + +.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png + :alt: Relationship between computeMatrix, heatmapper and profiler + + +You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix + + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd correctGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correctGCBias.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,108 @@ + + uses the output from computeGCBias to generate corrected BAM files + + + + correctGCBias + deepTools_macros.xml + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + + #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_bam_path = $temp_bam_handle.name + '.bam' + #silent $temp_bam_handle.close() + #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) + #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) + + + correctGCBias + + @THREADS@ + + --bamfile '$temp_bam_path' + --GCbiasFrequenciesFile $GCbiasFrequenciesFile + + @reference_genome_source@ + + + #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize + #else: + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt + #end if + + #if str($region).strip() != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + --binSize '$advancedOpt.binSize' + #end if + + ###set newoutFileName="corrected."+str($outFileFormat) + ##--correctedFile $newoutFileName; + --correctedFile "corrected.bam"; + + ##mv $newoutFileName $outFileName + mv "corrected.bam" $outFileName + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by +Benjamini and Speed (2012) Nucleic Acids Res. +The resulting BAM file can be used in any downstream analyses, but be aware that you should not filter out duplicates from here on. + +You can find more details on the correctGCBias wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias + + +**Output files**: + +- GC-normalized BAM file + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd deepTools_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,436 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + --numberOfProcessors "\${GALAXY_SLOTS:-4}" + + + @BINARY@ + samtools + deepTools + ucsc_tools + deepTools + ucsc_tools + numpy + pysam + scipy + matplotlib + samtools + bx-python + + + @BINARY@ --version + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #end if + + + + + + + + + + + + + + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + + +.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://github.com/fidelram/deepTools/wiki/ + + + + + + + + + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) + #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) + #silent $files.append('%s.bam' % $temp_input_path) + + ##set $files += [str($i.bamfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bamfile.name)] + #end if + #end for + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "${source.input1_2bit.fields.path}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r d2898b81b912 -r 2ad3b027dfcd heatmapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmapper.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,210 @@ + + creates a heatmap for a score associated to genomic regions + + + + heatmapper + deepTools_macros.xml + + + heatmapper + + --matrixFile $matrixFile + --outFileName $outFileName + + #if $output.showOutputSettings == "yes" + --plotFileFormat $output.outFileFormat + #if $outFileNameData: + --outFileNameData '$outFileNameData' + #end if + + #if $outFileNameMatrix: + --outFileNameMatrix '$outFileNameMatrix' + #end if + + #if $outFileSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #else + --plotFileFormat 'png' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes" + #if $advancedOpt.sortRegions: + --sortRegions '$advancedOpt.sortRegions' + #end if + + #if $advancedOpt.sortUsing: + --sortUsing '$advancedOpt.sortUsing' + #end if + + #if $advancedOpt.averageTypeSummaryPlot: + --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot' + #end if + + #if str($advancedOpt.missingDataColor.value) != "None": + --missingDataColor '$advancedOpt.missingDataColor' + #end if + + --colorMap '$advancedOpt.colorMap' + + #if $advancedOpt.zMin: + --zMin $advancedOpt.zMin + #end if + #if $advancedOpt.zMax: + --zMax $advancedOpt.zMax + #end if + + #if $advancedOpt.yMin: + --yMin $advancedOpt.yMin + #end if + #if $advancedOpt.yMax: + --yMax $advancedOpt.yMax + #end if + + --xAxisLabel '$advancedOpt.xAxisLabel' + --yAxisLabel '$advancedOpt.yAxisLabel' + + --heatmapWidth $advancedOpt.heatmapWidth + --heatmapHeight $advancedOpt.heatmapHeight + + --whatToShow '$advancedOpt.whatToShow' + + --startLabel '$advancedOpt.startLabel' + --endLabel '$advancedOpt.endLabel' + --refPointLabel '$advancedOpt.referencePointLabel' + --regionsLabel '$advancedOpt.regionsLabel' + + #if str($advancedOpt.plotTitle.value) != "None": + --plotTitle '$advancedOpt.plotTitle' + #end if + + $advancedOpt.onePlotPerGroup + + @kmeans_clusterin@ + + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. +Like profiler, it requires that computeMatrix was run first to calculate the values. + +We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as +with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of +groups with similar read distributions that you expect and the algorithm will do the sorting for you. + +Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows + + +.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png + :alt: Heatmap of RNA Polymerase II ChIP-seq + + +You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper + + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd profiler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profiler.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,163 @@ + + + creates a profile plot for a score associated to genomic regions + + + + + profiler + deepTools_macros.xml + + + profiler + + --matrixFile $matrixFile + --outFileName $outFileName + + #if $output.showOutputSettings == "yes" + --plotFileFormat $output.outFileFormat + + #if $output.saveData: + --outFileNameData '$outFileNameData' + #end if + + #if $output.saveSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #else + --plotFileFormat 'png' + #end if + + #if $scaleRegions.showScaleRegionsOpt == "yes": + --startLabel $scaleRegions.startLabel + --endLabel $scaleRegions.endLabel + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.averageType: + --averageType '$advancedOpt.averageType' + #end if + --plotHeight $advancedOpt.plotHeight + --plotWidth $advancedOpt.plotWidth + --plotType $advancedOpt.plotType + + --regionsLabel '$advancedOpt.regionsLabel' + + #if str($advancedOpt.plotTitle).strip() != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + + #if str($advancedOpt.colors).strip() != "": + --colors #echo ' '.join( ["'%s'" % $color for $color in $advancedOpt.colors.split()] )# + #end if + + $advancedOpt.onePlotPerGroup + + #if $advancedOpt.yMin: + --yMin $advancedOpt.yMin + #end if + #if $advancedOpt.yMax: + --yMax $advancedOpt.yMax + #end if + + --xAxisLabel '$advancedOpt.xAxisLabel' + #if str($advancedOpt.yAxisLabel.value) != "None": + --yAxisLabel '$advancedOpt.yAxisLabel' + #end if + + @kmeans_clusterin@ + + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value) + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool plots the average enrichments over all genomic +regions supplied to computeMarix. It requires that computeMatrix was successfully run. +It is a very useful complement to the heatmapper, especially in cases when you want to +compare the scores for many different groups. Like heatmapper, profiler does not change the +values that were compute by computeMatrix, but you can choose between +many different ways to color and display the plots. + + +.. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png + :alt: Meta-gene profile of Rna Polymerase II + + +You can find more details on the profiler wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler + + +----- + +@REFERENCES@ + + + diff -r d2898b81b912 -r 2ad3b027dfcd readme.rst --- a/readme.rst Tue Feb 04 13:45:17 2014 -0500 +++ b/readme.rst Thu Feb 06 06:40:05 2014 -0500 @@ -1,41 +1,61 @@ -This package contains a collection of Galaxy workflows utilising deepTools. +======================== +Galaxy deeptools wrapper +======================== -See http://www.galaxyproject.org for information about the Galaxy Project. +deepTools are user-friendly tools for the normalization and visualization of +deep-sequencing data. +They address the challenge of visualizing the large amounts of data that are now +routinely generated from sequencing centers in a meaningful way. +To do so, deepTools contain useful routines to process the mapped reads data +through removal of duplicates and different filtering options to create coverage +files in standard bedGraph and bigWig file formats. deepTools allow the creation +of normalized coverage files or the comparison between two files +(for example, treatment and control). Finally, using such normalized and +standardized files, multiple visualizations can be created to identify +enrichments with functional annotations of the genome. +For a gallery of images that can be produced and a description +of the tools see our poster_. + +.. _poster: http://f1000.com/posters/browse/summary/1094053 + +deeptools is developed under here: + + https://github.com/fidelram/deepTools + +For support, questions, or feature requests contact: deeptools@googlegroups.com -Sample Data -=========== - -Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you -can use aligned reads in BAM or SAM format. - - - +======== Citation ======== -If you use this workflow directly, or a derivative of it, or the associated -deepTools wrappers for Galaxy, in work leading to a scientific publication, -please cite: +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. + -{publication under review} +======= +History +======= + +- v1.0: Initial public release -Availability -============ +Licence (MIT) +============= -This workflow is available on the main Galaxy Tool Shed: - -http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows - -Development is being done on github: +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -https://github.com/fidelram/deepTools - +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -Dependencies -============ - -These dependencies should be resolved automatically via the Galaxy Tool Shed: - -* http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r d2898b81b912 -r 2ad3b027dfcd repository_dependencies.xml --- a/repository_dependencies.xml Tue Feb 04 13:45:17 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r d2898b81b912 -r 2ad3b027dfcd static/images/QC_GCplots_input.png Binary file static/images/QC_GCplots_input.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/QC_bamCorrelate_humanSamples.png Binary file static/images/QC_bamCorrelate_humanSamples.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/QC_fingerprint.png Binary file static/images/QC_fingerprint.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/flowChart_computeMatrixetc.png Binary file static/images/flowChart_computeMatrixetc.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/norm_IGVsnapshot_indFiles.png Binary file static/images/norm_IGVsnapshot_indFiles.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/visual_hm_DmelPolII.png Binary file static/images/visual_hm_DmelPolII.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd static/images/visual_profiler_DmelPolII.png Binary file static/images/visual_profiler_DmelPolII.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd test-data/master.mat.gz Binary file test-data/master.mat.gz has changed diff -r d2898b81b912 -r 2ad3b027dfcd test-data/master.png Binary file test-data/master.png has changed diff -r d2898b81b912 -r 2ad3b027dfcd test-data/test.bw Binary file test-data/test.bw has changed diff -r d2898b81b912 -r 2ad3b027dfcd test-data/test2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,8 @@ +ch1 100 150 CG11023 0 + +ch2 150 175 cda5 0 - +ch3 100 125 cda8 0 + +#Group 1 +ch1 75 125 C11023 0 + +ch2 125 150 ca5 0 - +ch3 75 100 ca8 0 + +#Group 2 diff -r d2898b81b912 -r 2ad3b027dfcd tool-data/deepTools_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/deepTools_seqs.loc.sample Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,27 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. You will +#need to supply these files and then create a deepTools_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The deepTools_seqs.loc +#file has this format: +# +# +# +#So, for example, if your deepTools_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your deepTools_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the is also used as "Species name abbreviation". diff -r d2898b81b912 -r 2ad3b027dfcd tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,7 @@ + + + + value, name, path + +
+ diff -r d2898b81b912 -r 2ad3b027dfcd tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Feb 06 06:40:05 2014 -0500 @@ -0,0 +1,101 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig + + + $INSTALL_DIR/bedGraphToBigWig + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo + + + $INSTALL_DIR/bigWigInfo + + + http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph + http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph + + + $INSTALL_DIR/bigWigToBedGraph + + + $INSTALL_DIR + + + + The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility. + + + + + + git clone --recursive https://github.com/fidelram/deepTools.git + + + + + + + + + + + + + + + + + + + git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b + $INSTALL_DIR/lib/python + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + $INSTALL_DIR/lib/python + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + + +