# HG changeset patch # User bgruening # Date 1517849128 18000 # Node ID 77e1664d66cdf87a7bad3582bbcc9306d0e15386 # Parent 5d11599b8a7ded207c5e00af492addf76ed47050 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c diff -r 5d11599b8a7d -r 77e1664d66cd deepTools_macros.xml --- a/deepTools_macros.xml Mon May 15 03:55:54 2017 -0400 +++ b/deepTools_macros.xml Mon Feb 05 11:45:28 2018 -0500 @@ -1,10 +1,10 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 2.5.1.1 + 2.5.7 - deeptools + deeptools @@ -211,7 +211,7 @@ - - - - - - - - - - - - - - - - - #if $advancedOpt.doExtendCustom.doExtend == 'custom': - --extendReads $advancedOpt.doExtendCustom.extendReadsValue - #else if $advancedOpt.doExtendCustom.doExtend == 'yes': - --extendReads - #end if - $advancedOpt.ignoreDuplicates - $advancedOpt.centerReads - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' - #end if - #if $advancedOpt.samFlagInclude: - --samFlagInclude $advancedOpt.samFlagInclude - #end if - #if $advancedOpt.samFlagExclude: - --samFlagExclude $advancedOpt.samFlagExclude - #end if - - - - - - - - - - - #if str($plotting_type.zMin) != "": - --zMin $plotting_type.zMin - #end if - #if str($plotting_type.zMax) != "": - --zMax $plotting_type.zMax - #end if - --colorMap '$plotting_type.colorMap' - $plotting_type.plotNumbers - --plotTitle '$plotting_type.plotTitle' - - - - - - - - - - - - - - - - - --numberOfProcessors "\${GALAXY_SLOTS:-4}" -<<<<<<< HEAD - 2.0.1.0 -======= - 2.1.0 ->>>>>>> d56067f86089e75354a2fad266002db3730766d9 - - - python - @BINARY@ -<<<<<<< HEAD - deepTools -======= - deepTools ->>>>>>> d56067f86089e75354a2fad266002db3730766d9 - - - - @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 - #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': - #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: - --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust - #end if - #end if - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: infomark - -For more information on the tools, please visit our `help site`_. - -If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com - -This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. - -.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac -.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de -.. _help site: https://deeptools.readthedocs.org/ - - - - - 10.1093/nar/gku365 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #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['saveSortedRegions'] is True - )) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 5d11599b8a7d -r 77e1664d66cd test-data/bamCoverage_result4.bg --- a/test-data/bamCoverage_result4.bg Mon May 15 03:55:54 2017 -0400 +++ b/test-data/bamCoverage_result4.bg Mon Feb 05 11:45:28 2018 -0500 @@ -1,472 +1,472 @@ -phiX174 0 10 16302.8 -phiX174 10 20 48908.5 -phiX174 20 70 146725 -phiX174 70 80 195634 -phiX174 80 90 179331 -phiX174 90 100 163028 -phiX174 100 120 114120 -phiX174 120 140 146725 -phiX174 140 150 163028 -phiX174 150 160 130423 -phiX174 160 170 163028 -phiX174 170 180 179331 -phiX174 180 200 211937 -phiX174 200 210 195634 -phiX174 210 220 244542 -phiX174 220 230 277148 -phiX174 230 240 342359 -phiX174 240 250 326057 -phiX174 250 260 293451 -phiX174 260 270 342359 -phiX174 270 280 407571 -phiX174 280 300 423874 -phiX174 300 310 358662 -phiX174 310 320 326057 -phiX174 320 330 374965 -phiX174 330 340 358662 -phiX174 340 350 293451 -phiX174 350 360 260845 -phiX174 360 370 228240 -phiX174 370 380 244542 -phiX174 380 390 309754 -phiX174 390 400 260845 -phiX174 400 410 244542 -phiX174 410 420 228240 -phiX174 420 450 293451 -phiX174 450 460 309754 -phiX174 460 470 342359 -phiX174 470 490 423874 -phiX174 490 510 505388 -phiX174 510 520 472782 -phiX174 520 530 570599 -phiX174 530 540 505388 -phiX174 540 550 537993 -phiX174 550 560 554296 -phiX174 560 570 652113 -phiX174 570 580 635810 -phiX174 580 590 570599 -phiX174 590 600 619508 -phiX174 600 610 554296 -phiX174 610 630 635810 -phiX174 630 640 586902 -phiX174 640 650 521691 -phiX174 650 660 554296 -phiX174 660 670 570599 -phiX174 670 680 603205 -phiX174 680 690 668416 -phiX174 690 700 652113 -phiX174 700 710 570599 -phiX174 710 730 603205 -phiX174 730 740 521691 -phiX174 740 760 603205 -phiX174 760 770 505388 -phiX174 770 780 521691 -phiX174 780 790 537993 -phiX174 790 800 554296 -phiX174 800 810 456479 -phiX174 810 820 440176 -phiX174 820 830 374965 -phiX174 830 840 326057 -phiX174 840 850 358662 -phiX174 850 860 309754 -phiX174 860 870 342359 -phiX174 870 880 260845 -phiX174 880 890 358662 -phiX174 890 900 391268 -phiX174 900 910 472782 -phiX174 910 920 554296 -phiX174 920 930 570599 -phiX174 930 940 554296 -phiX174 940 950 586902 -phiX174 950 960 603205 -phiX174 960 970 521691 -phiX174 970 980 489085 -phiX174 980 990 440176 -phiX174 990 1000 423874 -phiX174 1000 1010 456479 -phiX174 1010 1030 586902 -phiX174 1030 1040 766233 -phiX174 1040 1050 798839 -phiX174 1050 1060 831444 -phiX174 1060 1070 880353 -phiX174 1070 1080 847747 -phiX174 1080 1090 880353 -phiX174 1090 1100 782536 -phiX174 1100 1110 749930 -phiX174 1110 1120 668416 -phiX174 1120 1130 652113 -phiX174 1130 1140 635810 -phiX174 1140 1150 684719 -phiX174 1150 1160 635810 -phiX174 1160 1170 603205 -phiX174 1170 1180 619508 -phiX174 1180 1190 586902 -phiX174 1190 1200 521691 -phiX174 1200 1210 489085 -phiX174 1210 1220 570599 -phiX174 1220 1230 489085 -phiX174 1230 1240 456479 -phiX174 1240 1250 358662 -phiX174 1250 1260 342359 -phiX174 1260 1270 407571 -phiX174 1270 1280 358662 -phiX174 1280 1290 374965 -phiX174 1290 1300 326057 -phiX174 1300 1310 391268 -phiX174 1310 1320 521691 -phiX174 1320 1330 505388 -phiX174 1330 1340 521691 -phiX174 1340 1350 489085 -phiX174 1350 1370 505388 -phiX174 1370 1390 472782 -phiX174 1390 1400 358662 -phiX174 1400 1410 456479 -phiX174 1410 1430 489085 -phiX174 1430 1450 554296 -phiX174 1450 1460 570599 -phiX174 1460 1470 586902 -phiX174 1470 1480 619508 -phiX174 1480 1490 603205 -phiX174 1490 1500 554296 -phiX174 1500 1510 668416 -phiX174 1510 1520 635810 -phiX174 1520 1540 798839 -phiX174 1540 1550 733627 -phiX174 1550 1570 766233 -phiX174 1570 1580 782536 -phiX174 1580 1590 684719 -phiX174 1590 1600 635810 -phiX174 1600 1610 570599 -phiX174 1610 1620 537993 -phiX174 1620 1630 505388 -phiX174 1630 1640 472782 -phiX174 1640 1650 489085 -phiX174 1650 1660 505388 -phiX174 1660 1670 537993 -phiX174 1670 1680 603205 -phiX174 1680 1690 521691 -phiX174 1690 1700 537993 -phiX174 1700 1710 603205 -phiX174 1710 1720 554296 -phiX174 1720 1730 537993 -phiX174 1730 1740 586902 -phiX174 1740 1750 537993 -phiX174 1750 1760 440176 -phiX174 1760 1770 423874 -phiX174 1770 1780 374965 -phiX174 1780 1790 358662 -phiX174 1790 1810 342359 -phiX174 1810 1820 326057 -phiX174 1820 1830 472782 -phiX174 1830 1860 717325 -phiX174 1860 1870 815142 -phiX174 1870 1880 749930 -phiX174 1880 1890 684719 -phiX174 1890 1900 717325 -phiX174 1900 1910 619508 -phiX174 1910 1920 407571 -phiX174 1920 1930 472782 -phiX174 1930 1940 554296 -phiX174 1940 1950 456479 -phiX174 1950 1960 489085 -phiX174 1960 1970 537993 -phiX174 1970 1980 684719 -phiX174 1980 1990 652113 -phiX174 1990 2000 668416 -phiX174 2000 2010 684719 -phiX174 2010 2020 652113 -phiX174 2020 2030 668416 -phiX174 2030 2050 684719 -phiX174 2050 2060 489085 -phiX174 2060 2070 521691 -phiX174 2070 2080 489085 -phiX174 2080 2100 521691 -phiX174 2100 2110 537993 -phiX174 2110 2120 521691 -phiX174 2120 2130 537993 -phiX174 2130 2140 554296 -phiX174 2140 2150 521691 -phiX174 2150 2160 554296 -phiX174 2160 2170 423874 -phiX174 2170 2180 358662 -phiX174 2180 2190 440176 -phiX174 2190 2200 456479 -phiX174 2200 2210 440176 -phiX174 2210 2220 489085 -phiX174 2220 2230 554296 -phiX174 2230 2240 603205 -phiX174 2240 2250 635810 -phiX174 2250 2260 733627 -phiX174 2260 2270 635810 -phiX174 2270 2290 603205 -phiX174 2290 2300 619508 -phiX174 2300 2310 749930 -phiX174 2310 2320 782536 -phiX174 2320 2330 880353 -phiX174 2330 2340 864050 -phiX174 2340 2350 912959 -phiX174 2350 2360 815142 -phiX174 2360 2370 929261 -phiX174 2370 2380 815142 -phiX174 2380 2390 652113 -phiX174 2390 2400 603205 -phiX174 2400 2410 423874 -phiX174 2410 2420 407571 -phiX174 2420 2430 358662 -phiX174 2430 2440 489085 -phiX174 2440 2450 456479 -phiX174 2450 2460 619508 -phiX174 2460 2470 684719 -phiX174 2470 2480 749930 -phiX174 2480 2490 766233 -phiX174 2490 2500 782536 -phiX174 2500 2510 798839 -phiX174 2510 2520 652113 -phiX174 2520 2530 668416 -phiX174 2530 2540 537993 -phiX174 2540 2550 472782 -phiX174 2550 2560 391268 -phiX174 2560 2570 440176 -phiX174 2570 2590 472782 -phiX174 2590 2600 456479 -phiX174 2600 2620 537993 -phiX174 2620 2630 554296 -phiX174 2630 2640 701022 -phiX174 2640 2650 635810 -phiX174 2650 2660 570599 -phiX174 2660 2670 554296 -phiX174 2670 2680 619508 -phiX174 2680 2700 668416 -phiX174 2700 2710 635810 -phiX174 2710 2720 603205 -phiX174 2720 2740 668416 -phiX174 2740 2750 831444 -phiX174 2750 2760 880353 -phiX174 2760 2770 864050 -phiX174 2770 2780 896656 -phiX174 2780 2790 978170 -phiX174 2790 2800 831444 -phiX174 2800 2810 847747 -phiX174 2810 2820 815142 -phiX174 2820 2830 684719 -phiX174 2830 2840 717325 -phiX174 2840 2860 635810 -phiX174 2860 2870 619508 -phiX174 2870 2880 717325 -phiX174 2880 2890 668416 -phiX174 2890 2900 619508 -phiX174 2900 2910 668416 -phiX174 2910 2930 570599 -phiX174 2930 2940 521691 -phiX174 2940 2950 570599 -phiX174 2950 2960 505388 -phiX174 2960 2970 586902 -phiX174 2970 2980 603205 -phiX174 2980 2990 521691 -phiX174 2990 3000 537993 -phiX174 3000 3010 570599 -phiX174 3010 3020 521691 -phiX174 3020 3030 472782 -phiX174 3030 3040 440176 -phiX174 3040 3050 423874 -phiX174 3050 3060 554296 -phiX174 3060 3070 570599 -phiX174 3070 3080 635810 -phiX174 3080 3100 586902 -phiX174 3100 3110 733627 -phiX174 3110 3120 684719 -phiX174 3120 3130 652113 -phiX174 3130 3140 619508 -phiX174 3140 3160 684719 -phiX174 3160 3180 782536 -phiX174 3180 3190 717325 -phiX174 3190 3200 668416 -phiX174 3200 3210 684719 -phiX174 3210 3220 749930 -phiX174 3220 3230 668416 -phiX174 3230 3240 717325 -phiX174 3240 3250 635810 -phiX174 3250 3260 554296 -phiX174 3260 3270 603205 -phiX174 3270 3280 635810 -phiX174 3280 3290 586902 -phiX174 3290 3300 537993 -phiX174 3300 3310 521691 -phiX174 3310 3320 537993 -phiX174 3320 3330 619508 -phiX174 3330 3340 668416 -phiX174 3340 3370 652113 -phiX174 3370 3390 668416 -phiX174 3390 3400 586902 -phiX174 3400 3430 489085 -phiX174 3430 3440 521691 -phiX174 3440 3450 619508 -phiX174 3450 3460 586902 -phiX174 3460 3480 684719 -phiX174 3480 3490 733627 -phiX174 3490 3500 847747 -phiX174 3500 3510 815142 -phiX174 3510 3520 912959 -phiX174 3520 3530 782536 -phiX174 3530 3540 766233 -phiX174 3540 3550 798839 -phiX174 3550 3560 766233 -phiX174 3560 3570 701022 -phiX174 3570 3580 505388 -phiX174 3580 3590 472782 -phiX174 3590 3610 440176 -phiX174 3610 3620 423874 -phiX174 3620 3630 407571 -phiX174 3630 3640 391268 -phiX174 3640 3650 358662 -phiX174 3650 3660 440176 -phiX174 3660 3680 407571 -phiX174 3680 3690 423874 -phiX174 3690 3700 342359 -phiX174 3700 3710 391268 -phiX174 3710 3720 440176 -phiX174 3720 3730 635810 -phiX174 3730 3740 603205 -phiX174 3740 3750 717325 -phiX174 3750 3760 684719 -phiX174 3760 3780 668416 -phiX174 3780 3790 635810 -phiX174 3790 3800 505388 -phiX174 3800 3810 423874 -phiX174 3810 3820 456479 -phiX174 3820 3830 440176 -phiX174 3830 3840 554296 -phiX174 3840 3850 635810 -phiX174 3850 3860 782536 -phiX174 3860 3870 815142 -phiX174 3870 3880 782536 -phiX174 3880 3890 733627 -phiX174 3890 3900 684719 -phiX174 3900 3910 652113 -phiX174 3910 3920 603205 -phiX174 3920 3930 456479 -phiX174 3930 3950 407571 -phiX174 3950 3960 440176 -phiX174 3960 3970 537993 -phiX174 3970 3980 603205 -phiX174 3980 3990 570599 -phiX174 3990 4000 652113 -phiX174 4000 4010 635810 -phiX174 4010 4020 619508 -phiX174 4020 4030 652113 -phiX174 4030 4040 668416 -phiX174 4040 4050 554296 -phiX174 4050 4060 489085 -phiX174 4060 4070 456479 -phiX174 4070 4080 407571 -phiX174 4080 4090 440176 -phiX174 4090 4100 537993 -phiX174 4100 4110 407571 -phiX174 4110 4120 374965 -phiX174 4120 4130 309754 -phiX174 4130 4150 374965 -phiX174 4150 4160 342359 -phiX174 4160 4170 391268 -phiX174 4170 4180 277148 -phiX174 4180 4190 342359 -phiX174 4190 4200 358662 -phiX174 4200 4210 374965 -phiX174 4210 4230 326057 -phiX174 4230 4250 342359 -phiX174 4250 4260 391268 -phiX174 4260 4280 489085 -phiX174 4280 4290 456479 -phiX174 4290 4300 472782 -phiX174 4300 4310 537993 -phiX174 4310 4320 619508 -phiX174 4320 4330 586902 -phiX174 4330 4340 472782 -phiX174 4340 4350 423874 -phiX174 4350 4360 440176 -phiX174 4360 4380 521691 -phiX174 4380 4390 489085 -phiX174 4390 4400 456479 -phiX174 4400 4410 537993 -phiX174 4410 4420 668416 -phiX174 4420 4430 717325 -phiX174 4430 4440 798839 -phiX174 4440 4450 831444 -phiX174 4450 4460 815142 -phiX174 4460 4470 782536 -phiX174 4470 4480 798839 -phiX174 4480 4490 701022 -phiX174 4490 4500 635810 -phiX174 4500 4510 619508 -phiX174 4510 4520 472782 -phiX174 4520 4540 440176 -phiX174 4540 4550 505388 -phiX174 4550 4560 489085 -phiX174 4560 4570 440176 -phiX174 4570 4580 472782 -phiX174 4580 4590 423874 -phiX174 4590 4600 440176 -phiX174 4600 4610 537993 -phiX174 4610 4620 521691 -phiX174 4620 4630 586902 -phiX174 4630 4640 619508 -phiX174 4640 4660 701022 -phiX174 4660 4670 733627 -phiX174 4670 4680 684719 -phiX174 4680 4690 619508 -phiX174 4690 4700 701022 -phiX174 4700 4720 489085 -phiX174 4720 4730 407571 -phiX174 4730 4740 472782 -phiX174 4740 4760 570599 -phiX174 4760 4780 603205 -phiX174 4780 4790 619508 -phiX174 4790 4800 701022 -phiX174 4800 4810 684719 -phiX174 4810 4820 668416 -phiX174 4820 4830 603205 -phiX174 4830 4850 635810 -phiX174 4850 4860 586902 -phiX174 4860 4870 521691 -phiX174 4870 4880 505388 -phiX174 4880 4890 603205 -phiX174 4890 4900 521691 -phiX174 4900 4910 489085 -phiX174 4910 4920 423874 -phiX174 4920 4930 391268 -phiX174 4930 4950 358662 -phiX174 4950 4960 277148 -phiX174 4960 4970 179331 -phiX174 4970 4980 244542 -phiX174 4980 4990 211937 -phiX174 4990 5020 293451 -phiX174 5020 5030 358662 -phiX174 5030 5040 342359 -phiX174 5040 5050 374965 -phiX174 5050 5060 309754 -phiX174 5060 5070 293451 -phiX174 5070 5080 244542 -phiX174 5080 5090 309754 -phiX174 5090 5100 277148 -phiX174 5100 5110 228240 -phiX174 5110 5120 260845 -phiX174 5120 5130 326057 -phiX174 5130 5140 423874 -phiX174 5140 5160 505388 -phiX174 5160 5170 489085 -phiX174 5170 5180 586902 -phiX174 5180 5190 570599 -phiX174 5190 5200 537993 -phiX174 5200 5210 472782 -phiX174 5210 5220 456479 -phiX174 5220 5230 407571 -phiX174 5230 5240 456479 -phiX174 5240 5250 374965 -phiX174 5250 5260 277148 -phiX174 5260 5270 309754 -phiX174 5270 5280 342359 -phiX174 5280 5290 277148 -phiX174 5290 5300 195634 -phiX174 5300 5310 146725 -phiX174 5310 5340 97817 -phiX174 5340 5350 65211.3 -phiX174 5350 5386 32605.7 +phiX174 0 10 16038.5 +phiX174 10 20 48115.4 +phiX174 20 70 144346 +phiX174 70 80 192462 +phiX174 80 90 176423 +phiX174 90 100 160385 +phiX174 100 120 112269 +phiX174 120 140 144346 +phiX174 140 150 160385 +phiX174 150 160 128308 +phiX174 160 170 160385 +phiX174 170 180 176423 +phiX174 180 200 208500 +phiX174 200 210 192462 +phiX174 210 220 240577 +phiX174 220 230 272654 +phiX174 230 240 336808 +phiX174 240 250 320769 +phiX174 250 260 288692 +phiX174 260 270 336808 +phiX174 270 280 400962 +phiX174 280 300 417000 +phiX174 300 310 352846 +phiX174 310 320 320769 +phiX174 320 330 368885 +phiX174 330 340 352846 +phiX174 340 350 288692 +phiX174 350 360 256615 +phiX174 360 370 224538 +phiX174 370 380 240577 +phiX174 380 390 304731 +phiX174 390 400 256615 +phiX174 400 410 240577 +phiX174 410 420 224538 +phiX174 420 450 288692 +phiX174 450 460 304731 +phiX174 460 470 336808 +phiX174 470 490 417000 +phiX174 490 510 497192 +phiX174 510 520 465115 +phiX174 520 530 561346 +phiX174 530 540 497192 +phiX174 540 550 529269 +phiX174 550 560 545308 +phiX174 560 570 641538 +phiX174 570 580 625500 +phiX174 580 590 561346 +phiX174 590 600 609462 +phiX174 600 610 545308 +phiX174 610 630 625500 +phiX174 630 640 577385 +phiX174 640 650 513231 +phiX174 650 660 545308 +phiX174 660 670 561346 +phiX174 670 680 593423 +phiX174 680 690 657577 +phiX174 690 700 641538 +phiX174 700 710 561346 +phiX174 710 730 593423 +phiX174 730 740 513231 +phiX174 740 760 593423 +phiX174 760 770 497192 +phiX174 770 780 513231 +phiX174 780 790 529269 +phiX174 790 800 545308 +phiX174 800 810 449077 +phiX174 810 820 433038 +phiX174 820 830 368885 +phiX174 830 840 320769 +phiX174 840 850 352846 +phiX174 850 860 304731 +phiX174 860 870 336808 +phiX174 870 880 256615 +phiX174 880 890 352846 +phiX174 890 900 384923 +phiX174 900 910 465115 +phiX174 910 920 545308 +phiX174 920 930 561346 +phiX174 930 940 545308 +phiX174 940 950 577385 +phiX174 950 960 593423 +phiX174 960 970 513231 +phiX174 970 980 481154 +phiX174 980 990 433038 +phiX174 990 1000 417000 +phiX174 1000 1010 449077 +phiX174 1010 1030 577385 +phiX174 1030 1040 753808 +phiX174 1040 1050 785885 +phiX174 1050 1060 817962 +phiX174 1060 1070 866077 +phiX174 1070 1080 834000 +phiX174 1080 1090 866077 +phiX174 1090 1100 769846 +phiX174 1100 1110 737769 +phiX174 1110 1120 657577 +phiX174 1120 1130 641538 +phiX174 1130 1140 625500 +phiX174 1140 1150 673615 +phiX174 1150 1160 625500 +phiX174 1160 1170 593423 +phiX174 1170 1180 609462 +phiX174 1180 1190 577385 +phiX174 1190 1200 513231 +phiX174 1200 1210 481154 +phiX174 1210 1220 561346 +phiX174 1220 1230 481154 +phiX174 1230 1240 449077 +phiX174 1240 1250 352846 +phiX174 1250 1260 336808 +phiX174 1260 1270 400962 +phiX174 1270 1280 352846 +phiX174 1280 1290 368885 +phiX174 1290 1300 320769 +phiX174 1300 1310 384923 +phiX174 1310 1320 513231 +phiX174 1320 1330 497192 +phiX174 1330 1340 513231 +phiX174 1340 1350 481154 +phiX174 1350 1370 497192 +phiX174 1370 1390 465115 +phiX174 1390 1400 352846 +phiX174 1400 1410 449077 +phiX174 1410 1430 481154 +phiX174 1430 1450 545308 +phiX174 1450 1460 561346 +phiX174 1460 1470 577385 +phiX174 1470 1480 609462 +phiX174 1480 1490 593423 +phiX174 1490 1500 545308 +phiX174 1500 1510 657577 +phiX174 1510 1520 625500 +phiX174 1520 1540 785885 +phiX174 1540 1550 721731 +phiX174 1550 1570 753808 +phiX174 1570 1580 769846 +phiX174 1580 1590 673615 +phiX174 1590 1600 625500 +phiX174 1600 1610 561346 +phiX174 1610 1620 529269 +phiX174 1620 1630 497192 +phiX174 1630 1640 465115 +phiX174 1640 1650 481154 +phiX174 1650 1660 497192 +phiX174 1660 1670 529269 +phiX174 1670 1680 593423 +phiX174 1680 1690 513231 +phiX174 1690 1700 529269 +phiX174 1700 1710 593423 +phiX174 1710 1720 545308 +phiX174 1720 1730 529269 +phiX174 1730 1740 577385 +phiX174 1740 1750 529269 +phiX174 1750 1760 433038 +phiX174 1760 1770 417000 +phiX174 1770 1780 368885 +phiX174 1780 1790 352846 +phiX174 1790 1810 336808 +phiX174 1810 1820 320769 +phiX174 1820 1830 465115 +phiX174 1830 1860 705692 +phiX174 1860 1870 801923 +phiX174 1870 1880 737769 +phiX174 1880 1890 673615 +phiX174 1890 1900 705692 +phiX174 1900 1910 609462 +phiX174 1910 1920 400962 +phiX174 1920 1930 465115 +phiX174 1930 1940 545308 +phiX174 1940 1950 449077 +phiX174 1950 1960 481154 +phiX174 1960 1970 529269 +phiX174 1970 1980 673615 +phiX174 1980 1990 641538 +phiX174 1990 2000 657577 +phiX174 2000 2010 673615 +phiX174 2010 2020 641538 +phiX174 2020 2030 657577 +phiX174 2030 2050 673615 +phiX174 2050 2060 481154 +phiX174 2060 2070 513231 +phiX174 2070 2080 481154 +phiX174 2080 2100 513231 +phiX174 2100 2110 529269 +phiX174 2110 2120 513231 +phiX174 2120 2130 529269 +phiX174 2130 2140 545308 +phiX174 2140 2150 513231 +phiX174 2150 2160 545308 +phiX174 2160 2170 417000 +phiX174 2170 2180 352846 +phiX174 2180 2190 433038 +phiX174 2190 2200 449077 +phiX174 2200 2210 433038 +phiX174 2210 2220 481154 +phiX174 2220 2230 545308 +phiX174 2230 2240 593423 +phiX174 2240 2250 625500 +phiX174 2250 2260 721731 +phiX174 2260 2270 625500 +phiX174 2270 2290 593423 +phiX174 2290 2300 609462 +phiX174 2300 2310 737769 +phiX174 2310 2320 769846 +phiX174 2320 2330 866077 +phiX174 2330 2340 850038 +phiX174 2340 2350 898154 +phiX174 2350 2360 801923 +phiX174 2360 2370 914192 +phiX174 2370 2380 801923 +phiX174 2380 2390 641538 +phiX174 2390 2400 593423 +phiX174 2400 2410 417000 +phiX174 2410 2420 400962 +phiX174 2420 2430 352846 +phiX174 2430 2440 481154 +phiX174 2440 2450 449077 +phiX174 2450 2460 609462 +phiX174 2460 2470 673615 +phiX174 2470 2480 737769 +phiX174 2480 2490 753808 +phiX174 2490 2500 769846 +phiX174 2500 2510 785885 +phiX174 2510 2520 641538 +phiX174 2520 2530 657577 +phiX174 2530 2540 529269 +phiX174 2540 2550 465115 +phiX174 2550 2560 384923 +phiX174 2560 2570 433038 +phiX174 2570 2590 465115 +phiX174 2590 2600 449077 +phiX174 2600 2620 529269 +phiX174 2620 2630 545308 +phiX174 2630 2640 689654 +phiX174 2640 2650 625500 +phiX174 2650 2660 561346 +phiX174 2660 2670 545308 +phiX174 2670 2680 609462 +phiX174 2680 2700 657577 +phiX174 2700 2710 625500 +phiX174 2710 2720 593423 +phiX174 2720 2740 657577 +phiX174 2740 2750 817962 +phiX174 2750 2760 866077 +phiX174 2760 2770 850038 +phiX174 2770 2780 882115 +phiX174 2780 2790 962308 +phiX174 2790 2800 817962 +phiX174 2800 2810 834000 +phiX174 2810 2820 801923 +phiX174 2820 2830 673615 +phiX174 2830 2840 705692 +phiX174 2840 2860 625500 +phiX174 2860 2870 609462 +phiX174 2870 2880 705692 +phiX174 2880 2890 657577 +phiX174 2890 2900 609462 +phiX174 2900 2910 657577 +phiX174 2910 2930 561346 +phiX174 2930 2940 513231 +phiX174 2940 2950 561346 +phiX174 2950 2960 497192 +phiX174 2960 2970 577385 +phiX174 2970 2980 593423 +phiX174 2980 2990 513231 +phiX174 2990 3000 529269 +phiX174 3000 3010 561346 +phiX174 3010 3020 513231 +phiX174 3020 3030 465115 +phiX174 3030 3040 433038 +phiX174 3040 3050 417000 +phiX174 3050 3060 545308 +phiX174 3060 3070 561346 +phiX174 3070 3080 625500 +phiX174 3080 3100 577385 +phiX174 3100 3110 721731 +phiX174 3110 3120 673615 +phiX174 3120 3130 641538 +phiX174 3130 3140 609462 +phiX174 3140 3160 673615 +phiX174 3160 3180 769846 +phiX174 3180 3190 705692 +phiX174 3190 3200 657577 +phiX174 3200 3210 673615 +phiX174 3210 3220 737769 +phiX174 3220 3230 657577 +phiX174 3230 3240 705692 +phiX174 3240 3250 625500 +phiX174 3250 3260 545308 +phiX174 3260 3270 593423 +phiX174 3270 3280 625500 +phiX174 3280 3290 577385 +phiX174 3290 3300 529269 +phiX174 3300 3310 513231 +phiX174 3310 3320 529269 +phiX174 3320 3330 609462 +phiX174 3330 3340 657577 +phiX174 3340 3370 641538 +phiX174 3370 3390 657577 +phiX174 3390 3400 577385 +phiX174 3400 3430 481154 +phiX174 3430 3440 513231 +phiX174 3440 3450 609462 +phiX174 3450 3460 577385 +phiX174 3460 3480 673615 +phiX174 3480 3490 721731 +phiX174 3490 3500 834000 +phiX174 3500 3510 801923 +phiX174 3510 3520 898154 +phiX174 3520 3530 769846 +phiX174 3530 3540 753808 +phiX174 3540 3550 785885 +phiX174 3550 3560 753808 +phiX174 3560 3570 689654 +phiX174 3570 3580 497192 +phiX174 3580 3590 465115 +phiX174 3590 3610 433038 +phiX174 3610 3620 417000 +phiX174 3620 3630 400962 +phiX174 3630 3640 384923 +phiX174 3640 3650 352846 +phiX174 3650 3660 433038 +phiX174 3660 3680 400962 +phiX174 3680 3690 417000 +phiX174 3690 3700 336808 +phiX174 3700 3710 384923 +phiX174 3710 3720 433038 +phiX174 3720 3730 625500 +phiX174 3730 3740 593423 +phiX174 3740 3750 705692 +phiX174 3750 3760 673615 +phiX174 3760 3780 657577 +phiX174 3780 3790 625500 +phiX174 3790 3800 497192 +phiX174 3800 3810 417000 +phiX174 3810 3820 449077 +phiX174 3820 3830 433038 +phiX174 3830 3840 545308 +phiX174 3840 3850 625500 +phiX174 3850 3860 769846 +phiX174 3860 3870 801923 +phiX174 3870 3880 769846 +phiX174 3880 3890 721731 +phiX174 3890 3900 673615 +phiX174 3900 3910 641538 +phiX174 3910 3920 593423 +phiX174 3920 3930 449077 +phiX174 3930 3950 400962 +phiX174 3950 3960 433038 +phiX174 3960 3970 529269 +phiX174 3970 3980 593423 +phiX174 3980 3990 561346 +phiX174 3990 4000 641538 +phiX174 4000 4010 625500 +phiX174 4010 4020 609462 +phiX174 4020 4030 641538 +phiX174 4030 4040 657577 +phiX174 4040 4050 545308 +phiX174 4050 4060 481154 +phiX174 4060 4070 449077 +phiX174 4070 4080 400962 +phiX174 4080 4090 433038 +phiX174 4090 4100 529269 +phiX174 4100 4110 400962 +phiX174 4110 4120 368885 +phiX174 4120 4130 304731 +phiX174 4130 4150 368885 +phiX174 4150 4160 336808 +phiX174 4160 4170 384923 +phiX174 4170 4180 272654 +phiX174 4180 4190 336808 +phiX174 4190 4200 352846 +phiX174 4200 4210 368885 +phiX174 4210 4230 320769 +phiX174 4230 4250 336808 +phiX174 4250 4260 384923 +phiX174 4260 4280 481154 +phiX174 4280 4290 449077 +phiX174 4290 4300 465115 +phiX174 4300 4310 529269 +phiX174 4310 4320 609462 +phiX174 4320 4330 577385 +phiX174 4330 4340 465115 +phiX174 4340 4350 417000 +phiX174 4350 4360 433038 +phiX174 4360 4380 513231 +phiX174 4380 4390 481154 +phiX174 4390 4400 449077 +phiX174 4400 4410 529269 +phiX174 4410 4420 657577 +phiX174 4420 4430 705692 +phiX174 4430 4440 785885 +phiX174 4440 4450 817962 +phiX174 4450 4460 801923 +phiX174 4460 4470 769846 +phiX174 4470 4480 785885 +phiX174 4480 4490 689654 +phiX174 4490 4500 625500 +phiX174 4500 4510 609462 +phiX174 4510 4520 465115 +phiX174 4520 4540 433038 +phiX174 4540 4550 497192 +phiX174 4550 4560 481154 +phiX174 4560 4570 433038 +phiX174 4570 4580 465115 +phiX174 4580 4590 417000 +phiX174 4590 4600 433038 +phiX174 4600 4610 529269 +phiX174 4610 4620 513231 +phiX174 4620 4630 577385 +phiX174 4630 4640 609462 +phiX174 4640 4660 689654 +phiX174 4660 4670 721731 +phiX174 4670 4680 673615 +phiX174 4680 4690 609462 +phiX174 4690 4700 689654 +phiX174 4700 4720 481154 +phiX174 4720 4730 400962 +phiX174 4730 4740 465115 +phiX174 4740 4760 561346 +phiX174 4760 4780 593423 +phiX174 4780 4790 609462 +phiX174 4790 4800 689654 +phiX174 4800 4810 673615 +phiX174 4810 4820 657577 +phiX174 4820 4830 593423 +phiX174 4830 4850 625500 +phiX174 4850 4860 577385 +phiX174 4860 4870 513231 +phiX174 4870 4880 497192 +phiX174 4880 4890 593423 +phiX174 4890 4900 513231 +phiX174 4900 4910 481154 +phiX174 4910 4920 417000 +phiX174 4920 4930 384923 +phiX174 4930 4950 352846 +phiX174 4950 4960 272654 +phiX174 4960 4970 176423 +phiX174 4970 4980 240577 +phiX174 4980 4990 208500 +phiX174 4990 5020 288692 +phiX174 5020 5030 352846 +phiX174 5030 5040 336808 +phiX174 5040 5050 368885 +phiX174 5050 5060 304731 +phiX174 5060 5070 288692 +phiX174 5070 5080 240577 +phiX174 5080 5090 304731 +phiX174 5090 5100 272654 +phiX174 5100 5110 224538 +phiX174 5110 5120 256615 +phiX174 5120 5130 320769 +phiX174 5130 5140 417000 +phiX174 5140 5160 497192 +phiX174 5160 5170 481154 +phiX174 5170 5180 577385 +phiX174 5180 5190 561346 +phiX174 5190 5200 529269 +phiX174 5200 5210 465115 +phiX174 5210 5220 449077 +phiX174 5220 5230 400962 +phiX174 5230 5240 449077 +phiX174 5240 5250 368885 +phiX174 5250 5260 272654 +phiX174 5260 5270 304731 +phiX174 5270 5280 336808 +phiX174 5280 5290 272654 +phiX174 5290 5300 192462 +phiX174 5300 5310 144346 +phiX174 5310 5340 96230.8 +phiX174 5340 5350 64153.8 +phiX174 5350 5386 32076.9 diff -r 5d11599b8a7d -r 77e1664d66cd test-data/bamCoverage_result5.bw Binary file test-data/bamCoverage_result5.bw has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/bamPEFragmentSize_result1.txt --- a/test-data/bamPEFragmentSize_result1.txt Mon May 15 03:55:54 2017 -0400 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 05 11:45:28 2018 -0500 @@ -6,11 +6,11 @@ Fragment lengths: Min.: 241.0 1st Qu.: 241.5 -Mean: 244.666666667 +Mean: 244.66666666666666 Median: 242.0 3rd Qu.: 246.5 Max.: 251.0 -Std: 4.49691252108 +Std: 4.496912521077347 Read lengths: Min.: 251.0 diff -r 5d11599b8a7d -r 77e1664d66cd test-data/heatmapper_result1.png Binary file test-data/heatmapper_result1.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotCorrelation_result1.png Binary file test-data/plotCorrelation_result1.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotCorrelation_result2.png Binary file test-data/plotCorrelation_result2.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotCoverage_result1.png Binary file test-data/plotCoverage_result1.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotEnrichment_output.txt --- a/test-data/plotEnrichment_output.txt Mon May 15 03:55:54 2017 -0400 +++ b/test-data/plotEnrichment_output.txt Mon Feb 05 11:45:28 2018 -0500 @@ -1,5 +1,5 @@ file featureType percent +bowtie2 test1.bam up 100.00 bowtie2 test1.bam down 100.00 bowtie2 test1.bam up 100.00 bowtie2 test1.bam down 100.00 -bowtie2 test1.bam up 100.00 diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotFingerprint_quality_metrics.tabular --- a/test-data/plotFingerprint_quality_metrics.tabular Mon May 15 03:55:54 2017 -0400 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Feb 05 11:45:28 2018 -0500 @@ -1,3 +1,3 @@ Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269004498068 NA NA NA -bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 0.0 0.269004498068 0 0 0 +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 NA 0.26900449806812143 NA NA NA +bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.26900449806812143 0 0 0 diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotPCA_result1.png Binary file test-data/plotPCA_result1.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotPCA_result2.png Binary file test-data/plotPCA_result2.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/plotPCA_result2.tabular --- a/test-data/plotPCA_result2.tabular Mon May 15 03:55:54 2017 -0400 +++ b/test-data/plotPCA_result2.tabular Mon Feb 05 11:45:28 2018 -0500 @@ -1,3 +1,3 @@ Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue -1 -0.707106781187 -0.707106781187 6.0 -2 -0.707106781187 0.707106781187 1.23259516441e-32 +1 -0.7071067811865476 -0.7071067811865475 6.000000000000001 +2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32 diff -r 5d11599b8a7d -r 77e1664d66cd test-data/profiler_result1.png Binary file test-data/profiler_result1.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/profiler_result2.png Binary file test-data/profiler_result2.png has changed diff -r 5d11599b8a7d -r 77e1664d66cd test-data/profiler_result2.tabular --- a/test-data/profiler_result2.tabular Mon May 15 03:55:54 2017 -0400 +++ b/test-data/profiler_result2.tabular Mon Feb 05 11:45:28 2018 -0500 @@ -1,3 +1,3 @@ bin labels -0.0Kb 0.0Kb -bins 1 2 +bins 1.0 2.0 bamCoverage_result4_bw_0 genes 2477942.875 2610260.125