| Previous changeset 7:70bf1a5592be (2016-05-13) Next changeset 9:71385153e5d5 (2016-10-25) |
|
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe |
|
modified:
deepTools_macros.xml plotCoverage.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 |
|
added:
static/images/plotEnrichment_output.png test-data/plotEnrichment_output.png test-data/plotEnrichment_output.txt |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 deepTools_macros.xml --- a/deepTools_macros.xml Fri May 13 14:20:14 2016 -0400 +++ b/deepTools_macros.xml Tue Sep 20 03:02:08 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="${tool.name} image">\n <change_format>\n@@ -497,7 +595,9 @@\n </xml>\n \n <xml name="colorMap">\n- <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html">\n+ <param name="colorMap" type="select" label="Color map to use for the heatmap"\n+ help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"\n+ multiple="true">\n <option value="RdYlBu" selected="true">RdYlBu</option>\n <option value="Accent">Accent</option>\n <option value="Spectral">Spectral</option>\n' |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 plotCoverage.xml --- a/plotCoverage.xml Fri May 13 14:20:14 2016 -0400 +++ b/plotCoverage.xml Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -38,6 +38,7 @@ --plotTitle '$advancedOpt.plotTitle' #end if @ADVANCED_OPTS_READ_PROCESSING@ + @blacklist@ #end if ]]> @@ -60,6 +61,7 @@ <expand macro="read_processing_options" /> <expand macro="skipZeros" /> <expand macro="plotTitle" /> + <expand macro="blacklist" /> </when> </conditional> |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 static/images/plotEnrichment_output.png |
| b |
| Binary file static/images/plotEnrichment_output.png has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCompare_result1.bg --- a/test-data/bamCompare_result1.bg Fri May 13 14:20:14 2016 -0400 +++ b/test-data/bamCompare_result1.bg Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -1,1 +1,1 @@ -chrM 0 16569 1.0 +chrM 0 16569 1.00 |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result1.bw |
| b |
| Binary file test-data/bamCoverage_result1.bw has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result2.bw |
| b |
| Binary file test-data/bamCoverage_result2.bw has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result3.bg --- a/test-data/bamCoverage_result3.bg Fri May 13 14:20:14 2016 -0400 +++ b/test-data/bamCoverage_result3.bg Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Fri May 13 14:20:14 2016 -0400 +++ b/test-data/bamCoverage_result4.bg Tue Sep 20 03:02:08 2016 -0400 |
| b |
| b'@@ -1,472 +1,472 @@\n-phiX174\t0\t10\t16038.46\n-phiX174\t10\t20\t48115.38\n-phiX174\t20\t70\t144346.15\n-phiX174\t70\t80\t192461.54\n-phiX174\t80\t90\t176423.08\n-phiX174\t90\t100\t160384.62\n-phiX174\t100\t120\t112269.23\n-phiX174\t120\t140\t144346.15\n-phiX174\t140\t150\t160384.62\n-phiX174\t150\t160\t128307.69\n-phiX174\t160\t170\t160384.62\n-phiX174\t170\t180\t176423.08\n-phiX174\t180\t200\t208500.00\n-phiX174\t200\t210\t192461.54\n-phiX174\t210\t220\t240576.92\n-phiX174\t220\t230\t272653.85\n-phiX174\t230\t240\t336807.69\n-phiX174\t240\t250\t320769.23\n-phiX174\t250\t260\t288692.31\n-phiX174\t260\t270\t336807.69\n-phiX174\t270\t280\t400961.54\n-phiX174\t280\t300\t417000.00\n-phiX174\t300\t310\t352846.15\n-phiX174\t310\t320\t320769.23\n-phiX174\t320\t330\t368884.62\n-phiX174\t330\t340\t352846.15\n-phiX174\t340\t350\t288692.31\n-phiX174\t350\t360\t256615.38\n-phiX174\t360\t370\t224538.46\n-phiX174\t370\t380\t240576.92\n-phiX174\t380\t390\t304730.77\n-phiX174\t390\t400\t256615.38\n-phiX174\t400\t410\t240576.92\n-phiX174\t410\t420\t224538.46\n-phiX174\t420\t450\t288692.31\n-phiX174\t450\t460\t304730.77\n-phiX174\t460\t470\t336807.69\n-phiX174\t470\t490\t417000.00\n-phiX174\t490\t510\t497192.31\n-phiX174\t510\t520\t465115.38\n-phiX174\t520\t530\t561346.15\n-phiX174\t530\t540\t497192.31\n-phiX174\t540\t550\t529269.23\n-phiX174\t550\t560\t545307.69\n-phiX174\t560\t570\t641538.46\n-phiX174\t570\t580\t625500.00\n-phiX174\t580\t590\t561346.15\n-phiX174\t590\t600\t609461.54\n-phiX174\t600\t610\t545307.69\n-phiX174\t610\t630\t625500.00\n-phiX174\t630\t640\t577384.62\n-phiX174\t640\t650\t513230.77\n-phiX174\t650\t660\t545307.69\n-phiX174\t660\t670\t561346.15\n-phiX174\t670\t680\t593423.08\n-phiX174\t680\t690\t657576.92\n-phiX174\t690\t700\t641538.46\n-phiX174\t700\t710\t561346.15\n-phiX174\t710\t730\t593423.08\n-phiX174\t730\t740\t513230.77\n-phiX174\t740\t760\t593423.08\n-phiX174\t760\t770\t497192.31\n-phiX174\t770\t780\t513230.77\n-phiX174\t780\t790\t529269.23\n-phiX174\t790\t800\t545307.69\n-phiX174\t800\t810\t449076.92\n-phiX174\t810\t820\t433038.46\n-phiX174\t820\t830\t368884.62\n-phiX174\t830\t840\t320769.23\n-phiX174\t840\t850\t352846.15\n-phiX174\t850\t860\t304730.77\n-phiX174\t860\t870\t336807.69\n-phiX174\t870\t880\t256615.38\n-phiX174\t880\t890\t352846.15\n-phiX174\t890\t900\t384923.08\n-phiX174\t900\t910\t465115.38\n-phiX174\t910\t920\t545307.69\n-phiX174\t920\t930\t561346.15\n-phiX174\t930\t940\t545307.69\n-phiX174\t940\t950\t577384.62\n-phiX174\t950\t960\t593423.08\n-phiX174\t960\t970\t513230.77\n-phiX174\t970\t980\t481153.85\n-phiX174\t980\t990\t433038.46\n-phiX174\t990\t1000\t417000.00\n-phiX174\t1000\t1010\t449076.92\n-phiX174\t1010\t1030\t577384.62\n-phiX174\t1030\t1040\t753807.69\n-phiX174\t1040\t1050\t785884.62\n-phiX174\t1050\t1060\t817961.54\n-phiX174\t1060\t1070\t866076.92\n-phiX174\t1070\t1080\t834000.00\n-phiX174\t1080\t1090\t866076.92\n-phiX174\t1090\t1100\t769846.15\n-phiX174\t1100\t1110\t737769.23\n-phiX174\t1110\t1120\t657576.92\n-phiX174\t1120\t1130\t641538.46\n-phiX174\t1130\t1140\t625500.00\n-phiX174\t1140\t1150\t673615.38\n-phiX174\t1150\t1160\t625500.00\n-phiX174\t1160\t1170\t593423.08\n-phiX174\t1170\t1180\t609461.54\n-phiX174\t1180\t1190\t577384.62\n-phiX174\t1190\t1200\t513230.77\n-phiX174\t1200\t1210\t481153.85\n-phiX174\t1210\t1220\t561346.15\n-phiX174\t1220\t1230\t481153.85\n-phiX174\t1230\t1240\t449076.92\n-phiX174\t1240\t1250\t352846.15\n-phiX174\t1250\t1260\t336807.69\n-phiX174\t1260\t1270\t400961.54\n-phiX174\t1270\t1280\t352846.15\n-phiX174\t1280\t1290\t368884.62\n-phiX174\t1290\t1300\t320769.23\n-phiX174\t1300\t1310\t384923.08\n-phiX174\t1310\t1320\t513230.77\n-phiX174\t1320\t1330\t497192.31\n-phiX174\t1330\t1340\t513230.77\n-phiX174\t1340\t1350\t481153.85\n-phiX174\t1350\t1370\t497192.31\n-phiX174\t1370\t1390\t465115.38\n-phiX174\t1390\t1400\t352846.15\n-phiX174\t1400\t1410\t449076.92\n-phiX174\t1410\t1430\t481153.85\n-phiX174\t1430\t1450\t545307.69\n-phiX174\t1450\t1460\t561346.15\n-phiX174\t1460\t1470\t577384.62\n-phiX174\t1470\t1480\t609461.54\n-phiX174\t1480\t1490\t593423.08\n-phiX174\t1490\t1500\t545307.69\n-phiX174\t1500\t1510\t657576.92\n-phiX174\t1510\t1520\t625500.00\n-phiX174\t1520\t1540\t785884.62\n-phiX174\t1540\t1550\t721730.77\n-phiX174\t1550\t1570\t753807.69\n-phiX174\t1570\t1580\t769846.15\n-phiX174\t1580\t1590\t673615.38\n-phiX174\t1590\t1600\t625500.00\n-phiX174\t1600\t1610\t561346.15\n-phiX174\t1610\t1620\t529269.23\n-phiX174\t1620\t1630\t497192.31\n-phiX174\t1630\t1640\t465115.38\n-phiX174\t1640\t1650\t481153.85\n-phiX174\t1650\t1'..b'+phiX174\t3800\t3810\t423873.63\n+phiX174\t3810\t3820\t456479.29\n+phiX174\t3820\t3830\t440176.46\n+phiX174\t3830\t3840\t554296.28\n+phiX174\t3840\t3850\t635810.44\n+phiX174\t3850\t3860\t782535.93\n+phiX174\t3860\t3870\t815141.59\n+phiX174\t3870\t3880\t782535.93\n+phiX174\t3880\t3890\t733627.43\n+phiX174\t3890\t3900\t684718.93\n+phiX174\t3900\t3910\t652113.27\n+phiX174\t3910\t3920\t603204.78\n+phiX174\t3920\t3930\t456479.29\n+phiX174\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' |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result4.bw |
| b |
| Binary file test-data/bamCoverage_result4.bw has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamCoverage_result5.bw |
| b |
| Binary file test-data/bamCoverage_result5.bw has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamPEFragmentSize_histogram_result1.png |
| b |
| Binary file test-data/bamPEFragmentSize_histogram_result1.png has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Fri May 13 14:20:14 2016 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -1,6 +1,8 @@ + + +BAM file : 0.bam Sample size: 3 - Fragment lengths: Min.: 241.0 1st Qu.: 241.5 |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/correctGCBias_result1.bam |
| b |
| Binary file test-data/correctGCBias_result1.bam has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/plotEnrichment_output.png |
| b |
| Binary file test-data/plotEnrichment_output.png has changed |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/plotEnrichment_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 test-data/plotFingerprint_result2.tabular --- a/test-data/plotFingerprint_result2.tabular Fri May 13 14:20:14 2016 -0400 +++ b/test-data/plotFingerprint_result2.tabular Tue Sep 20 03:02:08 2016 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 70bf1a5592be -r 6fc072c36dc9 tool_dependencies.xml --- a/tool_dependencies.xml Fri May 13 14:20:14 2016 -0400 +++ b/tool_dependencies.xml Tue Sep 20 03:02:08 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> |
