| Previous changeset 7:b4886e1369c4 (2016-05-13) Next changeset 9:4efe24a9739e (2016-10-25) |
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Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe |
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modified:
bamPEFragmentSize.xml deepTools_macros.xml test-data/bamCompare_result1.bg test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/bamCoverage_result4.bg test-data/bamCoverage_result4.bw test-data/bamCoverage_result5.bw test-data/bamPEFragmentSize_histogram_result1.png test-data/bamPEFragmentSize_result1.txt test-data/correctGCBias_result1.bam test-data/plotFingerprint_result2.tabular tool_dependencies.xml |
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added:
static/images/plotEnrichment_output.png test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt |
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| diff -r b4886e1369c4 -r dc8d6e07d829 bamPEFragmentSize.xml --- a/bamPEFragmentSize.xml Fri May 13 13:53:21 2016 -0400 +++ b/bamPEFragmentSize.xml Mon Sep 19 17:25:47 2016 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> - <description>Estimate the predominant cDNA fragment length from a paired-end sequenced BAM file</description> + <description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM files</description> <macros> <token name="@BINARY@">bamPEFragmentSize</token> <import>deepTools_macros.xml</import> @@ -7,11 +7,13 @@ <expand macro="requirements" /> <command> <![CDATA[ - ln -s $bamInput one.bam && - ln -s '${bamInput.metadata.bam_index}' one.bam.bai && - + @multiple_input_bams@ @BINARY@ @THREADS@ + --bamfiles #echo " ".join($files) + #if $samplesLabel: + --samplesLabel #echo " ".join($samplesLabel) + #end if #if $histogram: --histogram ./hist.png #end if @@ -19,17 +21,27 @@ #if $advancedOpt.showAdvancedOpt == 'yes' --binSize '$advancedOpt.binSize' --distanceBetweenBins '$advancedOpt.distanceBetweenBins' + $advancedOpt.logScale + --maxFragmentLength '$advancedOpt.maxFragmentLength' + @blacklist@ #end if - one.bam > $outfile ]]> </command> <inputs> - <param name="bamInput" format="bam" type="data" label="BAM file" - help=""/> + <expand macro="multiple_input_bams" /> <param argument="--histogram" type="boolean" truevalue="--histogram" falsevalue="" label="Get the distribution of fragment lengths as a histogram" help=""/> + <param argument="--samplesLabel" type="text" size="30" + label="Labels for the samples (each BAM file) plotted" + help="The default is to use the file name of the sample. The sample labels should be separated by + spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> + <sanitizer> + <valid initial="string.printable"> + </valid> + </sanitizer> + </param> <expand macro="plotTitle" /> <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > @@ -43,6 +55,14 @@ <param argument="--distanceBetweenBins" type="integer" value="1000000" min="0" optional="true" label="bin spacing, in bases" help="To reduce the computation time, not every possible genomic bin is sampled. This option allows you to set the distance between bins actually sampled from. Larger numbers are sufficient for high coverage samples, while smaller values are useful for lower coverage samples. Note that if you specify a value that results in too few (<1000) reads sampled, the value will be decreased. (--distanceBetweenBins)"/> + <param argument="--logScale" type="boolean" truevalue="--logScale" falsevalue="" + label="Plot log frequencies" + help="Plot the frequencies on the log10 scale" /> + + <param argument="--maxFragmentLength" type="integer" min="0" value="0" + label="Maximum fragment length" + help="Maximum fragment length included in the histogram. A value of 0 (the default) denotes twice the mean fragment length" /> + <expand macro="blacklist" /> </when> </conditional> @@ -55,7 +75,7 @@ </outputs> <tests> <test> - <param name="bamInput" value="bowtie2 test1.bam" ftype="bam" /> + <param name="bamfiles" value="bowtie2 test1.bam" ftype="bam" /> <param name="histogram" value="True" /> <param name="plotTitle" value="Test Plot" /> <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> @@ -68,7 +88,7 @@ What it does ------------ -This tool samples a BAM file with paired-end data to estimate the fragment length distribution. +This tool samples the given BAM files with paired-end data to estimate the fragment length distribution. Properly paired reads are preferred for computation, i.e., unless a region does not contain any concordant pairs, discordant pairs are ignored. Output |
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| diff -r b4886e1369c4 -r dc8d6e07d829 deepTools_macros.xml --- a/deepTools_macros.xml Fri May 13 13:53:21 2016 -0400 +++ b/deepTools_macros.xml Mon Sep 19 17:25:47 2016 -0400 |
| [ |
| b'@@ -30,6 +30,25 @@\n #if $advancedOpt.samFlagExclude:\n --samFlagExclude $advancedOpt.samFlagExclude\n #end if\n+ #if $advancedOpt.minFragmentLength:\n+ --minFragmentLength $advancedOpt.minFragmentLength\n+ #end if\n+ #if $advancedOpt.maxFragmentLength:\n+ --maxFragmentLength $advancedOpt.maxFragmentLength\n+ #end if\n+ </token>\n+\n+ <token name="@ADVANCED_OPTS_GTF@">\n+ $advancedOpt.metagene\n+ #if $advancedOpt.transcriptID:\n+ --transcriptID $advancedOpt.transcriptID\n+ #end if\n+ #if $advancedOpt.exonID:\n+ --exonID $advancedOpt.exonID\n+ #end if\n+ #if $advancedOpt.transcript_id_designator:\n+ --transcript_id_designator $advancedOpt.transcript_id_designator\n+ #end if\n </token>\n \n <xml name="heatmap_options">\n@@ -59,9 +78,9 @@\n </xml>\n \n <xml name="zMin_zMax">\n- <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+ <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"\n help="If not specified the value is set automatically."/>\n- <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+ <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"\n help="If not specified the value is set automatically."/>\n </xml>\n \n@@ -72,18 +91,18 @@\n <sanitizer>\n <valid initial="string.letters,string.digits">\n <add value="|"/>\n+ <add value=":"/>\n </valid>\n </sanitizer>\n </param>\n </xml>\n \n <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n- <token name="@WRAPPER_VERSION@">2.2.3</token>\n+ <token name="@WRAPPER_VERSION@">2.3.5</token>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="2.7.10">python</requirement>\n- <requirement type="binary">@BINARY@</requirement>\n- <requirement type="package" version="2.2.3">deepTools</requirement>\n+ <requirement type="package" version="2.3.5">deepTools</requirement>\n <yield />\n </requirements>\n <expand macro="stdio" />\n@@ -159,14 +178,43 @@\n help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>\n </xml>\n \n+ <xml name="fragLength">\n+ <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"\n+ label="Minimum fragment length for inclusion."\n+ help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />\n+ <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"\n+ label="Maximum fragment length for inclusion."\n+ help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />\n+ </xml>\n+\n <xml name="read_processing_options">\n <expand macro="extendReads" />\n <expand macro="ignoreDuplicates" />\n <expand macro="centerReads" />\n <expand macro="minMappingQuality" />\n <expand macro="samFlags" />\n+ <expand macro="fragLength" />\n </xml>\n \n+ <xml name="gtf_options">\n+ <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""\n+ label="Use a metagene model"\n+ help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRN'..b'D/GTF format"\n+ help="One or more files containing regions to exclude from the analysis" />\n+ </xml>\n+\n+ <token name="@blacklist@">\n+<![CDATA[\n+ #if \' \'.join( map(str, $advancedOpt.blackListFileName) ) != \'None\':\n+ #set blfiles=[]\n+ #for $f in $advancedOpt.blackListFileName:\n+ #silent $blfiles.append("\'%s\'" % $f)\n+ #end for\n+ #if $blfiles != ["\'None\'"]:\n+ --blackListFileName #echo \' \'.join($blfiles)#\n+ #end if\n+ #end if\n+]]> \n+ </token>\n+\n+ <xml name="multiple_bed">\n+ <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"\n+ label="Regions in BED/GTF format"\n+ help="One or more files containing regions to include in the analysis" />\n+ </xml>\n+\n+ <token name="@multiple_bed@">\n+<![CDATA[\n+ #set files=[]\n+ #set labels=[]\n+ #for $f in $BED:\n+ #silent $files.append("\'%s\'" % $f)\n+ #silent $labels.append("\'%s\'" % $f.display_name)\n+ #end for\n+ #if len($files) > 0:\n+ --BED #echo \' \'.join($files)#\n+ --regionLabels #echo \' \'.join($labels)#\n+ #end if\n+]]> \n+ </token>\n+\n <xml name="reference_genome_source">\n <conditional name="source">\n <param name="ref_source" type="select" label="Reference genome">\n@@ -404,7 +493,8 @@\n <option value="specific">user specified</option>\n </param>\n <when value="specific">\n- <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n+ <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"\n+ help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>\n </when>\n <when value="2150570000" />\n <when value="2451960000" />\n@@ -439,7 +529,10 @@\n <when value="no" />\n <when value="yes">\n <yield />\n- <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ <param name="saveSortedRegions" type="boolean"\n+ label="Save the regions after skipping zeros or min/max threshold values"\n+ help="The order of the regions in the file follows the sorting order selected. This is useful,\n+ for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n </when>\n </conditional>\n </xml>\n@@ -454,6 +547,11 @@\n </param>\n </xml>\n \n+ <xml name="output_dpi">\n+ <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"\n+ label="Image dpi" help=""/>\n+ </xml>\n+\n <xml name="output_image_file_format">\n <data format="png" name="outFileName" label="${tool.name} image">\n <change_format>\n@@ -497,7 +595,9 @@\n </xml>\n \n <xml name="colorMap">\n- <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">\n+ <param name="colorMap" type="select" label="Color map to use for the heatmap"\n+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n+ multiple="true">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n' |
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| diff -r b4886e1369c4 -r dc8d6e07d829 static/images/plotEnrichment_output.png |
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| Binary file static/images/plotEnrichment_output.png has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Fri May 13 13:53:21 2016 -0400 +++ b/test-data/bamCompare_result1.bg Mon Sep 19 17:25:47 2016 -0400 |
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| @@ -1,1 +1,1 @@ -chrM 0 16569 1.0 +chrM 0 16569 1.00 |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCoverage_result1.bw |
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| Binary file test-data/bamCoverage_result1.bw has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Fri May 13 13:53:21 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Mon Sep 19 17:25:47 2016 -0400 |
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| @@ -1,8 +1,7 @@ -chrM 0 10 18498299.57 -chrM 10 200 9768764.94 -chrM 200 210 10184457.07 -chrM 210 220 9976611.00 +chrM 0 210 9768764.94 +chrM 210 220 9560918.88 chrM 220 230 7690304.31 -chrM 230 240 6027535.81 +chrM 230 240 5196151.56 chrM 240 250 3325537.00 chrM 250 260 623538.19 +chrM 260 16569 0.00 |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Fri May 13 13:53:21 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Sep 19 17:25:47 2016 -0400 |
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| b'@@ -1,472 +1,472 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t3930\t3950\t407570.79\n+phiX174\t3950\t3960\t440176.46\n+phiX174\t3960\t3970\t537993.45\n+phiX174\t3970\t3980\t603204.78\n+phiX174\t3980\t3990\t570599.11\n+phiX174\t3990\t4000\t652113.27\n+phiX174\t4000\t4010\t635810.44\n+phiX174\t4010\t4020\t619507.61\n+phiX174\t4020\t4030\t652113.27\n+phiX174\t4030\t4040\t668416.10\n+phiX174\t4040\t4050\t554296.28\n+phiX174\t4050\t4060\t489084.95\n+phiX174\t4060\t4070\t456479.29\n+phiX174\t4070\t4080\t407570.79\n+phiX174\t4080\t4090\t440176.46\n+phiX174\t4090\t4100\t537993.45\n+phiX174\t4100\t4110\t407570.79\n+phiX174\t4110\t4120\t374965.13\n+phiX174\t4120\t4130\t309753.80\n+phiX174\t4130\t4150\t374965.13\n+phiX174\t4150\t4160\t342359.47\n+phiX174\t4160\t4170\t391267.96\n+phiX174\t4170\t4180\t277148.14\n+phiX174\t4180\t4190\t342359.47\n+phiX174\t4190\t4200\t358662.30\n+phiX174\t4200\t4210\t374965.13\n+phiX174\t4210\t4230\t326056.64\n+phiX174\t4230\t4250\t342359.47\n+phiX174\t4250\t4260\t391267.96\n+phiX174\t4260\t4280\t489084.95\n+phiX174\t4280\t4290\t456479.29\n+phiX174\t4290\t4300\t472782.12\n+phiX174\t4300\t4310\t537993.45\n+phiX174\t4310\t4320\t619507.61\n+phiX174\t4320\t4330\t586901.94\n+phiX174\t4330\t4340\t472782.12\n+phiX174\t4340\t4350\t423873.63\n+phiX174\t4350\t4360\t440176.46\n+phiX174\t4360\t4380\t521690.62\n+phiX174\t4380\t4390\t489084.95\n+phiX174\t4390\t4400\t456479.29\n+phiX174\t4400\t4410\t537993.45\n+phiX174\t4410\t4420\t668416.10\n+phiX174\t4420\t4430\t717324.60\n+phiX174\t4430\t4440\t798838.76\n+phiX174\t4440\t4450\t831444.42\n+phiX174\t4450\t4460\t815141.59\n+phiX174\t4460\t4470\t782535.93\n+phiX174\t4470\t4480\t798838.76\n+phiX174\t4480\t4490\t701021.77\n+phiX174\t4490\t4500\t635810.44\n+phiX174\t4500\t4510\t619507.61\n+phiX174\t4510\t4520\t472782.12\n+phiX174\t4520\t4540\t440176.46\n+phiX174\t4540\t4550\t505387.79\n+phiX174\t4550\t4560\t489084.95\n+phiX174\t4560\t4570\t440176.46\n+phiX174\t4570\t4580\t472782.12\n+phiX174\t4580\t4590\t423873.63\n+phiX174\t4590\t4600\t440176.46\n+phiX174\t4600\t4610\t537993.45\n+phiX174\t4610\t4620\t521690.62\n+phiX174\t4620\t4630\t586901.94\n+phiX174\t4630\t4640\t619507.61\n+phiX174\t4640\t4660\t701021.77\n+phiX174\t4660\t4670\t733627.43\n+phiX174\t4670\t4680\t684718.93\n+phiX174\t4680\t4690\t619507.61\n+phiX174\t4690\t4700\t701021.77\n+phiX174\t4700\t4720\t489084.95\n+phiX174\t4720\t4730\t407570.79\n+phiX174\t4730\t4740\t472782.12\n+phiX174\t4740\t4760\t570599.11\n+phiX174\t4760\t4780\t603204.78\n+phiX174\t4780\t4790\t619507.61\n+phiX174\t4790\t4800\t701021.77\n+phiX174\t4800\t4810\t684718.93\n+phiX174\t4810\t4820\t668416.10\n+phiX174\t4820\t4830\t603204.78\n+phiX174\t4830\t4850\t635810.44\n+phiX174\t4850\t4860\t586901.94\n+phiX174\t4860\t4870\t521690.62\n+phiX174\t4870\t4880\t505387.79\n+phiX174\t4880\t4890\t603204.78\n+phiX174\t4890\t4900\t521690.62\n+phiX174\t4900\t4910\t489084.95\n+phiX174\t4910\t4920\t423873.63\n+phiX174\t4920\t4930\t391267.96\n+phiX174\t4930\t4950\t358662.30\n+phiX174\t4950\t4960\t277148.14\n+phiX174\t4960\t4970\t179331.15\n+phiX174\t4970\t4980\t244542.48\n+phiX174\t4980\t4990\t211936.81\n+phiX174\t4990\t5020\t293450.97\n+phiX174\t5020\t5030\t358662.30\n+phiX174\t5030\t5040\t342359.47\n+phiX174\t5040\t5050\t374965.13\n+phiX174\t5050\t5060\t309753.80\n+phiX174\t5060\t5070\t293450.97\n+phiX174\t5070\t5080\t244542.48\n+phiX174\t5080\t5090\t309753.80\n+phiX174\t5090\t5100\t277148.14\n+phiX174\t5100\t5110\t228239.64\n+phiX174\t5110\t5120\t260845.31\n+phiX174\t5120\t5130\t326056.64\n+phiX174\t5130\t5140\t423873.63\n+phiX174\t5140\t5160\t505387.79\n+phiX174\t5160\t5170\t489084.95\n+phiX174\t5170\t5180\t586901.94\n+phiX174\t5180\t5190\t570599.11\n+phiX174\t5190\t5200\t537993.45\n+phiX174\t5200\t5210\t472782.12\n+phiX174\t5210\t5220\t456479.29\n+phiX174\t5220\t5230\t407570.79\n+phiX174\t5230\t5240\t456479.29\n+phiX174\t5240\t5250\t374965.13\n+phiX174\t5250\t5260\t277148.14\n+phiX174\t5260\t5270\t309753.80\n+phiX174\t5270\t5280\t342359.47\n+phiX174\t5280\t5290\t277148.14\n+phiX174\t5290\t5300\t195633.98\n+phiX174\t5300\t5310\t146725.49\n+phiX174\t5310\t5340\t97816.99\n+phiX174\t5340\t5350\t65211.33\n+phiX174\t5350\t5386\t32605.66\n' 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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| Binary file test-data/bamCoverage_result5.bw has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamPEFragmentSize_histogram_result1.png |
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| Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 13:53:21 2016 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Sep 19 17:25:47 2016 -0400 |
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| @@ -1,6 +1,8 @@ + + +BAM file : 0.bam Sample size: 3 - Fragment lengths: Min.: 241.0 1st Qu.: 241.5 |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/plotEnrichment_output.png |
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| Binary file test-data/plotEnrichment_output.png has changed |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/plotEnrichment_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Mon Sep 19 17:25:47 2016 -0400 |
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| @@ -0,0 +1,5 @@ +file featureType percent +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 |
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| diff -r b4886e1369c4 -r dc8d6e07d829 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Fri May 13 13:53:21 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Mon Sep 19 17:25:47 2016 -0400 |
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| @@ -1,239 +1,239 @@ 'bowtie2 test1.bam' 'bowtie2 test1.bam' -68 68 -65 65 -61 61 -57 57 -43 43 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -37 37 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -35 35 -29 29 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +35 35 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 +33 33 27 27 -26 26 -22 22 +25 25 +24 24 21 21 20 20 -20 20 +19 19 +19 19 19 19 17 17 17 17 |
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| diff -r b4886e1369c4 -r dc8d6e07d829 tool_dependencies.xml --- a/tool_dependencies.xml Fri May 13 13:53:21 2016 -0400 +++ b/tool_dependencies.xml Mon Sep 19 17:25:47 2016 -0400 |
| b |
| @@ -3,7 +3,7 @@ <package name="python" version="2.7.10"> <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="deepTools" version="2.2.3"> - <repository changeset_revision="2f4601e4fc32" name="package_python_2_7_deeptools_2_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="2.3.5"> + <repository changeset_revision="c3e87c8140fe" name="package_python_2_7_deeptools_2_3_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |
