# HG changeset patch # User iuc # Date 1392496864 18000 # Node ID d9a0a017896a4100d7c61e7ca9abffa349dd8f75 # Parent d89001e78ee4d0c05d01a369c3a79b9be5549e5a Uploaded diff -r d89001e78ee4 -r d9a0a017896a bamCompare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCompare.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,222 @@ + + 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 in the `bamCompare wiki`_. + +.. _bamCompare wiki: 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 d89001e78ee4 -r d9a0a017896a bamCorrelate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCorrelate.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,169 @@ + + 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 is computed for all +pairs of BAM files. + + +.. image:: $PATH_TO_IMAGES/QC_bamCorrelate_humanSamples.png + :alt: Heatmap of RNA Polymerase II ChIP-seq + + +You can find more details in the `bamCorrelate wiki`_. + +.. _bamCorrelate wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCompare + + +**Output files**: + +- diagnostic plot produced by bamCorrelate is a clustered heatmap displaying the values for each pair-wise correlation, see below for an example +- data matrix (optional) in case you want to plot the correlation values using a different program, e.g. R, this matrix can be used + + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a bamCoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamCoverage.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,159 @@ + + generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig) + + + + bamCoverage + deepTools_macros.xml + + + bamCoverage + + @THREADS@ + + --bam '$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 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 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:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png + + +You can find more details in the `bamCoverage wiki`_. + +.. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage + + +**Output files**: + +- coverage file either in bigWig or bedGraph format + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a bamFingerprint.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamFingerprint.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,151 @@ + + plots profiles of BAM files; useful for assesing ChIP signal strength + + + + bamFingerprint + deepTools_macros.xml + + + @multiple_input_bams@ + + bamFingerprint + + @THREADS@ + + --bamfiles #echo " ".join($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 based on a method developed by Diaz et al. (2012). Stat Appl Genet Mol Biol 11(3). +The resulting plot can be used to assess the strength of a ChIP (for factors that bind to narrow regions). +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 and the cumulative sum of read counts are plotted. An ideal input +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 in the `bamFingerprint wiki`_. + +.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint + + +**Output files**: + +- Diagnostic plot +- Data matrix of raw counts + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a computeGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeGCBias.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,157 @@ + + 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 in the `computeGCBias wiki`_. + +.. _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 d89001e78ee4 -r d9a0a017896a computeMatrix.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrix.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,221 @@ + + 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 summarizes and prepares an intermediary file +containing 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. This tool can also be used to filter and sort +regions according to their score. + + +.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png + :alt: Relationship between computeMatrix, heatmapper and profiler + + +You can find more details in the `computeMatrix wiki`_. + +.. _computeMatrix wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix + + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a correctGCBias.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/correctGCBias.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,109 @@ + + 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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool requires the output from computeGCBias to correct the given BAM files according to the method proposed by Benjamini and Speed (2012). Nucleic Acids Res. +The resulting BAM files 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 in the `correctGCBias wiki`_. + +.. _correctGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-correctGCbias + + +**Output files**: + +- GC-normalized BAM file + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a deepTools_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml Sat Feb 15 15:41:04 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 informations, please visit the `project 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 +.. _project 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 d89001e78ee4 -r d9a0a017896a dir2html.py --- a/dir2html.py Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#!/usr/bin/env python -import os -import sys -from xml.sax.saxutils import escape - -def make_table( directory ): - ret = ['\n'] - for file in os.listdir( directory ): - ret.append('\n' % ( file, escape(file).replace( 'MACS2_', '' ) )) - ret.append('
%s
') - return ''.join(ret) - -def make_html( directory, stderr ): - return '\n'.join(['' - '', - ' Additional output created by MACS2', - ' ', - '', - '', - '

Additional Files:

', - make_table( directory ), - '

Messages from MACS2:

', - stderr.read().replace('\n', '
'), - '', - '']) - -if __name__ == '__main__': - if len(sys.argv) == 3: - directory_path = sys.argv[1] - stderr = open( sys.argv[2] ) - print make_html( directory_path, stderr ) - else: - sys.exit( 'Two parameter expected: directory path and stderr path' ) - diff -r d89001e78ee4 -r d9a0a017896a heatmapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmapper.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,211 @@ + + 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. +Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. +In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; +it can also be generated separately by the tool profiler). +We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as +with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, +e.g. one plot per chromosome, simply supply each group as an individual BED file. + + +.. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png + :alt: Heatmap of RNA Polymerase II ChIP-seq + + +You can find more details in the `heatmapper wiki`_. + +.. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper + + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a macs2_bdgbroadcall.xml --- a/macs2_bdgbroadcall.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,42 +0,0 @@ - - Call broad peaks from bedGraph output - - - - macs2_macros.xml - - - macs2 bdgbroadcall - --ifile $infile - --cutoff-peak $cutoffpeak - --cutoff-link $cutofflink - --min-length $minlen - --lvl1-max-gap $LVL1MAXGAP - --lvl2-max-gap $LVL2MAXGAP - --ofile $ofile - - - - - - - - - - - - - - - - - - -**What it does** - -Call broad peaks from bedGraph output. -bdgbroadcall from macs2 - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_bdgcmp.xml --- a/macs2_bdgcmp.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,78 +0,0 @@ - - Deduct noise by comparing two signal tracks in bedGraph - - - - macs2_macros.xml - - - macs2 bdgcmp - -t $input_treatment_file - -c $input_control_file - - -m $bdgcmp_options.bdgcmp_options_selector - #if $bdgcmp_options.bdgcmp_options_selector in ['FE', 'logFR', 'logLR']: - -p $pseudocount - #end if - --ofile $ofile - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) -is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for -identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of -binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. - -View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README - ------- - -**Usage** - -**Peak Calling**: Main MACS2 Function to Call peaks from alignment results. - -**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. - - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_bdgdiff.xml --- a/macs2_bdgdiff.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ - - Differential peak detection based on paired four bedgraph files - - - - macs2_macros.xml - - - macs2 bdgdiff - --t1 $infile_pileup_cond1 - --t2 $infile_pileup_cond2 - --c1 $infile_control_cond1 - --c2 $infile_control_cond2 - --cutoff $cutoff - --min-len $minlen - --depth1 $depth1 - --depth2 $depth2 - - # Why does #if '--ofile-cond1' in $outputs not work? - #if '--ofile-cond1' in str($outputs).split(','): - --ofile-cond1 $output_cond1 - #end if - - #if '--ofile-cond2' in str($outputs).split(','): - --ofile-cond2 $output_cond2 - #end if - - #if '--ofile-both-conditions' in str($outputs).split(','): - --ofile-both-conditions $output_both - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - '--ofile-cond1' in outputs - - - '--ofile-cond2' in outputs - - - '--ofile-both-conditions' in outputs - - - - - - -**What it does** - -bdgdiff from macs2 - - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_bdgpeakcall.xml --- a/macs2_bdgpeakcall.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ - - Call peaks from bedGraph output - - - - macs2_macros.xml - - - macs2 bdgpeakcall - --ifile $infile - --cutoff $cutoff - --min-length $minlen - --max-gap $maxgap - $callsummits - $notrackline - --ofile $ofile - - - - - - - - - - - - - - - - - - - -**What it does** - -Call peaks from bedGraph output. -bdgpeakcall from macs2 - - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_callpeak.xml --- a/macs2_callpeak.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,208 +0,0 @@ - - Call peaks from alignment results - - R_3_0_1 - MACS2_SCRIPT_PATH - - - - macs2_macros.xml - - - #import os - #set $temp_stderr = 'macs2_stderr' - macs2 callpeak - - --name "MACS2" - -t #echo ' '.join( map(str, $input_treatment_file) )# - - #if ' '.join( map(str, $input_control_file) ) != 'None': - -c #echo ' '.join( map(str, $input_control_file) )# - #end if - - #for $ifile in $input_treatment_file: - --format='$ifile.ext.upper()' - #end for - - @effective_genome_size@ - - --bw='$band_width' - - ## advanced options - #if str( $advanced_options.advanced_options_selector ) == 'on': - --mfold $advanced_options.mfoldlo $advanced_options.mfoldhi - $advanced_options.nolambda - - #if str($advanced_options.broad_options.broad_options_selector) == '--broad': - --broad - --broad-cutoff='$advanced_options.broad_options.broad_cutoff' - #end if - - #else: - ## set default parameter - --mfold 10 30 - #end if - - ## With --bdg two additional output files will be generated. - #if 'bdg' in str($outputs).split(','): - --bdg - #end if - - ## pq value select options - #if str( $pq_options.pq_options_selector ) == 'qvalue': - --qvalue $pq_options.qvalue - #else: - --pvalue $pq_options.pvalue - #end if - - ## model options - #if str( $nomodel_type.nomodel_type_selector ) == 'nomodel': - --nomodel --shiftsize='$nomodel_type.shiftsize' - #end if - - 2> $temp_stderr; - - ## run R to create pdf from model script - #if 'pdf' in str($outputs).split(','): - Rscript MACS2_model.r > MACS2_model.r.log; - #end if - - #if 'html' in str($outputs).split(','): - ## if output files exists, move them to the extra_files_path and create a html result page linking to them - count=`ls -1 MACS2* 2>/dev/null | wc -l`; - if [ \$count != 0 ]; - then - mkdir $output_extra_files.extra_files_path; - cp MACS2* $output_extra_files.extra_files_path; - python \$MACS2_SCRIPT_PATH/dir2html.py $output_extra_files.extra_files_path $temp_stderr > $output_extra_files; - fi; - #end if - - cat $temp_stderr 2>&1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'peaks_bed' in outputs - - - 'narrow' in outputs - - - - (( - advanced_options['advanced_options_selector'] == "on" and - advanced_options['broad_options']['broad_options_selector'] == "--broad" - )) - - - - 'summits' in outputs - - - 'pdf' in outputs - - - 'bdg' in outputs - - - 'bdg' in outputs - - - 'html' in outputs - - - - - - -**What it does** - -With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) -is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for -identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of -binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. - -View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README - ------- - -**Usage** - -**Peak Calling**: Main MACS2 Function to Call peaks from alignment results. - -If you choose "Scores in bedGraph files" MACS will output the fragment pileup, control lambda, -log10-pvalue and -log10-qvalue scores in bedGraph files. - - -**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. - - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_filterdup.xml --- a/macs2_filterdup.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,59 +0,0 @@ - - Remove duplicate reads at the same position - - - - macs2_macros.xml - - - macs2 filterdup - -t $infile - -o $outfile - - --format '$ifile.extension.upper()' - --gsize $gsize - @tag_size@ - --pvalue $pvalue - #if str( $keep_dup_options.keep_dup_options_selector ) == "user": - --keep-dup $keep_dup_options.user_keepdup - #else - --keep-dup str( $keep_dup_options.keep_dup_options_selector ) - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -Remove duplicate reads at the same position, then convert acceptable format to BED format. -filterdup tool from macs2 - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_macros.xml --- a/macs2_macros.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ - - - - macs2 - numpy - - - - - - - - - - - - - - - - - - - - - #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined': - --gsize $effective_genome_size_options.gsize - #else: - --gsize $effective_genome_size_options.effective_genome_size_options_selector - #end if - - - - macs2 --version - - - - - - - #if $tsize == -1.0: - --tsize $tsize - #end if - - - - - - - - - - - - ------- - -**Citation** - -For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. - -Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening. - - diff -r d89001e78ee4 -r d9a0a017896a macs2_predictd.xml --- a/macs2_predictd.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ - - Predict 'd' or fragment size from alignment results - - R_3_0_1 - - - - macs2_macros.xml - - - macs2 predictd - -i #echo ','.join( map( str, $infiles) )# - @tag_size@ - @effective_genome_size@ - --bw $band_width - --mfold $mfoldlo $mfoldhi - > $outfile; - - Rscript predicted_model.R > $outfile_image - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -bdgdiff from macs2 - - -Note that pair-end data is not supposed to work with this command. - - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_randsample.xml --- a/macs2_randsample.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ - - Randomly sample number or percentage of total reads - - - - macs2_macros.xml - - - macs2 randsample - -t $infile - -o $outfile - - --format '$ifile.extension.upper()' - - @tag_size@ - #if str($method_options.method_options_selector ) == 'percentage': - $method_options.percentage - #else: - $method_options.number - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**What it does** - -randsample tool from macs2 - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a macs2_refinepeak.xml --- a/macs2_refinepeak.xml Fri Jan 24 11:18:29 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - - Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) - - - - macs2_macros.xml - - - macs2 refinepeak - -b $bed_infile - -i $infile - --format '$ifile.extension.upper()' - --cutoff $cutoff - --window-size $winsize - --ofile $ofile - - - - - - - - - - - - - - - - -**What it does** - -(Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP. - -@citation@ - - diff -r d89001e78ee4 -r d9a0a017896a profiler.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profiler.xml Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,165 @@ + + + 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 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 in the `profiler wiki`_. + +.. _profiler wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-profiler + + +----- + +@REFERENCES@ + + + diff -r d89001e78ee4 -r d9a0a017896a readme.rst --- a/readme.rst Fri Jan 24 11:18:29 2014 -0500 +++ b/readme.rst Sat Feb 15 15:41:04 2014 -0500 @@ -1,60 +1,61 @@ ======================== -Galaxy wrapper for MACS2 +Galaxy deeptools wrapper ======================== -With the improvement of sequencing techniques, chromatin immunoprecipitation -followed by high throughput sequencing (ChIP-Seq) is getting popular to study -genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq -analysis method, we present a novel algorithm, named Model-based Analysis of -ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures -the influence of genome complexity to evaluate the significance of enriched ChIP -regions, and MACS improves the spatial resolution of binding sites through -combining the information of both sequencing tag position and orientation. -MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. +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 -============ -Installation -============ +======== +Citation +======== -It is recommended to install this wrapper via the `Galaxy Tool Shed`. - -.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. ======= History ======= -- v2.0.10.1: Initial public release -- v2.0.10.3: add "broad peaks" options - -==================== -Detailed description -==================== - -View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst +- v1.0: Initial public release -=============================== -Wrapper Licence (MIT/BSD style) -=============================== +Licence (MIT) +============= + +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: -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. - +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 d89001e78ee4 -r d9a0a017896a static/images/QC_GCplots_input.png Binary file static/images/QC_GCplots_input.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/QC_bamCorrelate_humanSamples.png Binary file static/images/QC_bamCorrelate_humanSamples.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/QC_fingerprint.png Binary file static/images/QC_fingerprint.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/flowChart_computeMatrixetc.png Binary file static/images/flowChart_computeMatrixetc.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/norm_IGVsnapshot_indFiles.png Binary file static/images/norm_IGVsnapshot_indFiles.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/visual_hm_DmelPolII.png Binary file static/images/visual_hm_DmelPolII.png has changed diff -r d89001e78ee4 -r d9a0a017896a static/images/visual_profiler_DmelPolII.png Binary file static/images/visual_profiler_DmelPolII.png has changed diff -r d89001e78ee4 -r d9a0a017896a test-data/master.mat.gz Binary file test-data/master.mat.gz has changed diff -r d89001e78ee4 -r d9a0a017896a test-data/master.png Binary file test-data/master.png has changed diff -r d89001e78ee4 -r d9a0a017896a test-data/test.bw Binary file test-data/test.bw has changed diff -r d89001e78ee4 -r d9a0a017896a test-data/test2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.bed Sat Feb 15 15:41:04 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 d89001e78ee4 -r d9a0a017896a tool-data/deepTools_seqs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/deepTools_seqs.loc.sample Sat Feb 15 15:41:04 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 d89001e78ee4 -r d9a0a017896a tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Feb 15 15:41:04 2014 -0500 @@ -0,0 +1,7 @@ + + + + value, name, path + +
+ diff -r d89001e78ee4 -r d9a0a017896a tool_dependencies.xml --- a/tool_dependencies.xml Fri Jan 24 11:18:29 2014 -0500 +++ b/tool_dependencies.xml Sat Feb 15 15:41:04 2014 -0500 @@ -1,51 +1,101 @@ + + + - + + + + - + - - + + - - $REPOSITORY_INSTALL_DIR - - - + + + + + - git clone --recursive https://github.com/taoliu/MACS.git - - ../MACS - git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb - git submodule update --recursive + + 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/lib/python - $ENV[PYTHONPATH_NUMPY] - $ENV[PATH_NUMPY] $INSTALL_DIR/bin - $ENV[PYTHONPATH_SCIPY] - $INSTALL_DIR/lib/python - - - - Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS - + $INSTALL_DIR/lib/python + + TRUE + + + + + Installation of deepTools from Fidel Ramirez. + https://github.com/fidelram/deepTools + +