| Previous changeset 7:d5d57b40b29a (2016-05-13) Next changeset 9:6aee99aec0d1 (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:
bamCompare.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 d5d57b40b29a -r 89f6d2283317 bamCompare.xml --- a/bamCompare.xml Fri May 13 14:34:30 2016 -0400 +++ b/bamCompare.xml Tue Sep 20 03:06:21 2016 -0400 |
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| @@ -65,6 +65,8 @@ #if str($advancedOpt.ignoreForNormalization).strip() != '': --ignoreForNormalization '$advancedOpt.ignoreForNormalization' #end if + + @blacklist@ #end if ]]> </command> @@ -105,12 +107,16 @@ label="How to compare the two files" help="The default is to output the log2ratio between the two samples. The reciprocal ratio returns the negative of the inverse of the ratio if - the ratio is less than 0. The resulting values are interpreted as negative fold changes."> + the ratio is less than 0. The resulting values are interpreted as negative + fold changes. To output the scaled values from the first or second BAM file, + select 'first' or 'second'."> <option value="log2" selected="true">Compute log2 of the number of reads ratio</option> <option value="ratio">Compute the ratio of the number of reads</option> <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option> <option value="add">Compute the sum of number of reads</option> <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option> + <option value="first">Returns the scaled value of the first BAM file</option> + <option value="second">Returns the scaled value of the second BAM file</option> </param> <when value="log2"> <expand macro="pseudocount" /> @@ -119,6 +125,8 @@ <expand macro="pseudocount" /> </when> <when value="add" /> + <when value="first" /> + <when value="second" /> <when value="reciprocal_ratio"> <expand macro="pseudocount" /> </when> @@ -154,12 +162,14 @@ <expand macro="read_processing_options" /> <expand macro="skipNAs" /> + <param argument="--ignoreForNormalization" type="text" value="" size="50" label="regions that should be excluded for calculating the scaling factor" help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know of copy number variations between samples then you may want to exclude these. Another typical example is the difference in chromosome X copies between males and females in many species. Example inputs are chrX,chrY,chr3 or chr10:12220-128932" /> + <expand macro="blacklist" /> </when> </conditional> </inputs> |
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| diff -r d5d57b40b29a -r 89f6d2283317 deepTools_macros.xml --- a/deepTools_macros.xml Fri May 13 14:34:30 2016 -0400 +++ b/deepTools_macros.xml Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 static/images/plotEnrichment_output.png |
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| Binary file static/images/plotEnrichment_output.png has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Fri May 13 14:34:30 2016 -0400 +++ b/test-data/bamCompare_result1.bg Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 test-data/bamCoverage_result1.bw |
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| Binary file test-data/bamCoverage_result1.bw has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 test-data/bamCoverage_result2.bw |
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| Binary file test-data/bamCoverage_result2.bw has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Fri May 13 14:34:30 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Fri May 13 14:34:30 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 test-data/bamCoverage_result4.bw |
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| Binary file test-data/bamCoverage_result4.bw has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 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 d5d57b40b29a -r 89f6d2283317 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 14:34:30 2016 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 test-data/correctGCBias_result1.bam |
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| Binary file test-data/correctGCBias_result1.bam has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 test-data/plotEnrichment_output.png |
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| Binary file test-data/plotEnrichment_output.png has changed |
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| diff -r d5d57b40b29a -r 89f6d2283317 test-data/plotEnrichment_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Fri May 13 14:34:30 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Tue Sep 20 03:06:21 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 d5d57b40b29a -r 89f6d2283317 tool_dependencies.xml --- a/tool_dependencies.xml Fri May 13 14:34:30 2016 -0400 +++ b/tool_dependencies.xml Tue Sep 20 03:06:21 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> |
