Mercurial > repos > bgruening > hicexplorer_hicnormalize
changeset 9:f34ab9882252 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
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--- a/hicNormalize.xml Wed Oct 18 10:21:43 2023 +0000 +++ b/hicNormalize.xml Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>normalizes a matrix to norm range or smallest read count</description> <macros> <token name="@BINARY@">hicNormalize</token>
--- a/macros.xml Wed Oct 18 10:21:43 2023 +0000 +++ b/macros.xml Mon Jul 01 19:55:26 2024 +0000 @@ -1,7 +1,8 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@TOOL_VERSION@">3.7.2</token> + <token name="@TOOL_VERSION@">3.7.5</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $use_range.range_min:$use_range.range_max @@ -248,7 +249,7 @@ #set $matrices = [] #set $mlabels = [] #for $counter, $i in enumerate($input_files): - ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; + ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext'; #silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext)) #if str($i.mlabel.value) != "":
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.2 +# Created with chicQualityControl version 3.7.5 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix. # Used Matrices 0_matrix.cool 1_matrix.cool # Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.2 +# Created with chicQualityControl version 3.7.5 # QC report for matrices: 0_matrix.cool 1_matrix.cool #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
--- a/test-data/cHi-C/target_list.bed Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/cHi-C/target_list.bed Mon Jul 01 19:55:26 2024 +0000 @@ -1,8 +1,8 @@ -chr1 4480000 4549000 -chr1 4555000 4688000 -chr1 14274000 14279000 -chr1 14290000 14439000 -chr1 14444000 14467000 -chr1 14476000 14501000 -chr1 19077000 19118000 -chr1 19120000 19274000 \ No newline at end of file +chr1 4480000 4549000 +chr1 4555000 4688000 +chr1 14274000 14279000 +chr1 14290000 14439000 +chr1 14444000 14467000 +chr1 14476000 14501000 +chr1 19077000 19118000 +chr1 19120000 19274000
--- a/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.2 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 # H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. # Accepted regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one # Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
--- a/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.2 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 # H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one # Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
--- a/test-data/hicHyperoptDetectLoops/loops.bedgraph Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph Mon Jul 01 19:55:26 2024 +0000 @@ -1,3 +1,3 @@ -# Created by HiCExplorer hicHyperoptDetectLoops 3.6 +# Created by HiCExplorer hicHyperoptDetectLoops 3.7.3 -{'matrixFile': 'matrix.cool', 'maxLoopDistance': 2600000, 'maximumNumberOfLoops': 5, 'oet': 4.594451600287669, 'p': 0.07561093779253786, 'peakWidth': 2, 'pit': 68.07931954714506, 'pp': 0.021875258449572325, 'proteinFile': 'hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak', 'resolution': 2, 'threads': 1, 'windowSize': 10} \ No newline at end of file +{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 2300000, 'maximumNumberOfLoops': 5, 'oet': 1.230889168935347, 'p': 0.048940366161874596, 'peakWidth': 6, 'pit': 22.88867979095296, 'pp': 0.13365961880597724, 'proteinFile': '/tmp/tmpjkr0wi60/files/6/a/7/dataset_6a78c4eb-7f74-459b-9ed8-08972cc0c5f4.dat', 'resolution': 2, 'threads': 1, 'windowSize': 6} \ No newline at end of file
--- a/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2 +# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5 File: matrix_name.h5 Size: 33,754 Bin_length: 5000
--- a/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,22 +1,22 @@ -# Created with HiCExplorer's hicInterIntraTAD version 3.7.2 +# Created with HiCExplorer's hicInterIntraTAD version 3.7.5 # Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio -chr2 17100000 18100000 region_0 0 + 0 148.64980341892507 0 1.0 0 90 0 90 289.00804022517053 100 100 1.0 0.0 0.5143448718696884 0.5143448718696884 -chr2 18100000 19100000 region_1 0 + 162.1124908492847 211.04026046280666 1.0 1.0 100 140 100 140 277.9356647725957 100 100 1.0 0.583273438412172 0.7593133491359512 1.3425867875481232 -chr2 19100000 20600000 region_2 0 + 223.14353637851622 150.01947633135822 1.0 1.0 150 90 150 90 556.143932925097 225 225 1.0 0.4012334274777925 0.269749371430369 0.6709827989081616 -chr2 20600000 21300000 region_3 0 + 171.34866125986417 274.4679914622871 1.0 1.0 105 84 105 84 149.85761183392816 49 49 1.0 1.1434097952244984 1.8315251931710472 2.9749349883955456 -chr2 21300000 22600000 region_4 0 + 283.89289960594425 768.874984677404 1.0 1.0 91 208 91 208 24180.36424789467 169 169 1.0 0.011740637845464306 0.03179749390021485 0.04353813174567915 -chr2 22600000 24300000 region_5 0 + 789.804014201572 321.70053830625835 1.0 1.0 221 238 221 238 659.9593561049022 289 289 1.0 1.1967464464221198 0.48745507633219043 1.6842015227543101 -chr2 24300000 25800000 region_6 0 + 340.44705127228065 836.790681935677 1.0 1.0 255 720 255 720 598.8884085354028 225 225 1.0 0.5684649200422041 1.3972397361673277 1.965704656209532 -chr2 25800000 30700000 region_7 0 + 852.3657188383157 1593.0953595672838 1.0 1.0 735 1421 735 1421 4153.286346671477 2401 2401 1.0 0.20522681262307327 0.3835746506724779 0.5888014632955512 -chr2 30700000 33700000 region_8 0 + 1644.3620053137968 315.02407146145276 1.0 1.0 1470 240 1470 240 1873.0714290428866 900 900 1.0 0.8778960480722525 0.16818582920910052 1.046081877281353 -chr2 33700000 34600000 region_9 0 + 351.38600814451206 204.32883091037917 1.0 1.0 270 153 270 153 245.00889544594847 81 81 1.0 1.434176532672184 0.8339649486541041 2.268141481326288 -chr2 34600000 36400000 region_10 0 + 213.88883777381795 379.5343566721307 1.0 1.0 162 288 162 288 770.6376988509402 324 324 1.0 0.27754785172427593 0.49249388816305717 0.7700417398873332 -chr2 36400000 38100000 region_11 0 + 399.4783208321819 189.4340956757372 1.0 1.0 306 136 306 136 635.9658356069232 289 289 1.0 0.6281443097504547 0.29786835246417603 0.9260126622146307 -chr2 38100000 39000000 region_12 0 + 209.82145375215833 74.59004956153072 1.0 1.0 153 45 153 45 229.67774089590498 81 81 1.0 0.9135471854334115 0.3247595925951596 1.2383067780285713 -chr2 39000000 39600000 region_13 0 + 87.2296637584025 120.04828267162685 1.0 1.0 54 72 54 72 114.2377217834551 36 36 1.0 0.7635802114799864 1.0508637672168046 1.814443978696791 -chr2 39600000 40900000 region_14 0 + 127.68593516818584 348.8073054441913 1.0 1.0 78 247 78 247 447.58733970743407 169 169 1.0 0.2852760206569915 0.7793055667575172 1.0645815874145086 -chr2 40900000 42900000 region_15 0 + 363.6155543954171 330.73139298156053 1.0 1.0 260 240 260 240 912.1015373488856 400 400 1.0 0.3986568813953566 0.3626037008367121 0.7612605822320687 -chr2 42900000 44200000 region_16 0 + 353.76150800590995 305.3562724757596 1.0 1.0 260 208 260 208 434.0150296605763 169 169 1.0 0.8150904550069866 0.7035615165552332 1.51865197156222 -chr2 44200000 45900000 region_17 0 + 321.3851510623236 309.7368872510572 1.0 1.0 221 221 221 221 667.4121186463332 289 289 1.0 0.4815392799791639 0.4640863996885097 0.9456256796676736 -chr2 45900000 47300000 region_18 0 + 330.1441180225245 330.3028710611577 1.0 1.0 238 238 238 238 509.86032585858186 196 196 1.0 0.6475187444062777 0.6478301101481911 1.2953488545544687 -chr2 47300000 49100000 region_19 0 + 330.3028710611577 0 1.0 0 238 0 238 0 737.4495555644096 324 324 1.0 0.44789893568836614 0.0 0.44789893568836614 +chr2 17100000 18100000 ID_0.01_10 -0.230354 . 0 148.64979 0 1.0 0 90 0 90 289.00809 100 100 1.0 0.0 0.5143447368549441 0.5143447368549441 +chr2 18100000 19100000 ID_0.01_11 -0.5135365 . 162.11248 211.04027000000002 1.0 1.0 100 140 100 140 277.9356 100 100 1.0 0.5832735353081793 0.7593135604075189 1.3425870957156982 +chr2 19100000 20600000 ID_0.01_12 -0.4202525 . 223.14355000000003 150.01946 1.0 1.0 150 90 150 90 556.14405 225 225 1.0 0.4012333675061345 0.2697492852795962 0.6709826527857307 +chr2 20600000 21300000 ID_0.01_13 -0.9980865 . 171.34865000000002 274.46791 1.0 1.0 105 84 105 84 149.85761000000002 49 49 1.0 1.1434097340802378 1.8315246719869613 2.974934406067199 +chr2 21300000 22600000 ID_0.01_14 -0.859866 . 283.89281 768.8750100000001 1.0 1.0 91 208 91 208 24180.409890000003 169 169 1.0 0.01174061197851762 0.031797434927601224 0.043538046906118844 +chr2 22600000 24300000 ID_0.01_15 -0.281294 . 789.8040400000002 321.70053 1.0 1.0 221 238 221 238 659.9594400000001 289 289 1.0 1.1967463333807304 0.48745500178010936 1.6842013351608398 +chr2 24300000 25800000 ID_0.01_16 -1.0366175 . 340.44703 836.7906700000001 1.0 1.0 255 720 255 720 598.88844 225 225 1.0 0.5684648546564032 1.397239642828972 1.9657044974853752 +chr2 25800000 30700000 ID_0.01_17 -0.1471245 . 852.3657199999999 1593.09544 1.0 1.0 735 1421 735 1421 4153.28651 2401 2401 1.0 0.205226804832205 0.38357465495439663 0.5888014597866016 +chr2 30700000 33700000 ID_0.01_18 -1.0134455 . 1644.36207 315.02405 1.0 1.0 1470 240 1470 240 1873.0712400000002 900 900 1.0 0.877896171210231 0.16818583472564555 1.0460820059358766 +chr2 33700000 34600000 ID_0.01_19 -1.33809 . 351.38599999999997 204.32889000000003 1.0 1.0 270 153 270 153 245.00895 81 81 1.0 1.4341761800946453 0.8339650041355633 2.268141184230209 +chr2 34600000 36400000 ID_0.01_20 -0.6325015 . 213.88889999999998 379.5344099999999 1.0 1.0 162 288 162 288 770.63772 324 324 1.0 0.27754792485371726 0.4924939438469219 0.7700418687006392 +chr2 36400000 38100000 ID_0.01_21 -0.925006 . 399.4784 189.43412 1.0 1.0 306 136 306 136 635.96573 289 289 1.0 0.6281445385429809 0.2978684401752277 0.9260129787182088 +chr2 38100000 39000000 ID_0.01_22 -0.911804 . 209.82147 74.59004 1.0 1.0 153 45 153 45 229.67774999999997 81 81 1.0 0.9135472199636231 0.3247595380919571 1.2383067580555802 +chr2 39000000 39600000 ID_0.01_23 -0.474157 . 87.22966 120.04826999999999 1.0 1.0 54 72 54 72 114.23772 36 36 1.0 0.7635801905010009 1.05086367269935 1.8144438632003508 +chr2 39600000 40900000 ID_0.01_24 -0.483398 . 127.68592 348.8071999999999 1.0 1.0 78 247 78 247 447.58727999999996 169 169 1.0 0.28527602482358305 0.7793054351321154 1.0645814599556984 +chr2 40900000 42900000 ID_0.01_25 -0.7016145 . 363.61542999999995 330.73137999999994 1.0 1.0 260 240 260 240 912.1014799999999 400 400 1.0 0.3986567700778207 0.362603709403037 0.7612604794808577 +chr2 42900000 44200000 ID_0.01_26 -0.6584895 . 353.76149 305.35633 1.0 1.0 260 208 260 208 434.01493999999997 169 169 1.0 0.8150905819048533 0.7035617944396109 1.5186523763444641 +chr2 44200000 45900000 ID_0.01_27 -1.4067435 . 321.38521000000003 309.73695 1.0 1.0 221 221 221 221 667.4121100000001 289 289 1.0 0.4815393745252839 0.46408649971904153 0.9456258742443254 +chr2 45900000 47300000 ID_0.01_28 -0.656308 . 330.14417000000003 330.30287 1.0 1.0 238 238 238 238 509.86028 196 196 1.0 0.6475189045908814 0.647830166334981 1.2953490709258624 +chr2 47300000 49100000 ID_0.01_29 -0.0033885 . 330.30287 0 1.0 0 238 0 238 0 737.44951 324 324 1.0 0.4478989619235085 0.0 0.4478989619235085
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--- a/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.2 +# Created with HiCExplorer's hicPlotSVL 3.7.5 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum # Short range contacts: <= 2000000 0_small_test_matrix.h5 1_small_test_matrix.h5 1.0
--- a/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Mon Jul 01 19:55:26 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.2 +# Created with HiCExplorer's hicPlotSVL 3.7.5 # Short range vs long range contacts per chromosome: raw data # Short range contacts: <= 2000000 # 0_small_test_matrix.h5 1_small_test_matrix.h5
--- a/test-data/hicQuickQC/QC.log Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicQuickQC/QC.log Mon Jul 01 19:55:26 2024 +0000 @@ -1,5 +1,5 @@ -File /var/folders/nm/9sgmbhhj6gn_h8b308xvhm0w0000gt/T/tmp8sucpx99.h5 +File /tmp/tmpjkr0wi60/tmp/tmp8o_td4fd.h5 Sequenced reads 983 Min rest. site distance 300 Max library insert size 1000
--- a/test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed Wed Oct 18 10:21:43 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -chr2L 800001 1550001 ID_0.01_1 0.022884658057 . 800001 1550001 31,120,180 -chr2L 1550001 2100001 ID_0.01_2 -0.744086372037 . 1550001 2100001 51,160,44 -chr2L 2100001 2400001 ID_0.01_3 0.311391232701 . 2100001 2400001 31,120,180 -chr2L 2400001 2750001 ID_0.01_4 0.078149036231 . 2400001 2750001 51,160,44 -chr2L 2750001 3700001 ID_0.01_5 -0.648971714281 . 2750001 3700001 31,120,180 -chr2L 3700001 4200001 ID_0.01_6 -0.133385571846 . 3700001 4200001 51,160,44 -chr2L 4200001 5050001 ID_0.01_7 -0.598347187435 . 4200001 5050001 31,120,180 -chr2L 5050001 5450001 ID_0.01_8 -0.589296128895 . 5050001 5450001 51,160,44 -chr2L 5450001 6550001 ID_0.01_9 -0.463215188679 . 5450001 6550001 31,120,180 -chr2L 6550001 7250001 ID_0.01_10 -0.739312227247 . 6550001 7250001 51,160,44 -chr2L 7250001 7650001 ID_0.01_11 -0.558267533146 . 7250001 7650001 31,120,180 -chr2L 7650001 8100001 ID_0.01_12 -0.164474310036 . 7650001 8100001 51,160,44 -chr2L 8100001 8950001 ID_0.01_13 -0.618832592666 . 8100001 8950001 31,120,180 -chr2L 8950001 10450001 ID_0.01_14 -0.547147684409 . 8950001 10450001 51,160,44 -chr2L 10450001 10800001 ID_0.01_15 -0.938748995456 . 10450001 10800001 31,120,180 -chr2L 10800001 11600001 ID_0.01_16 -0.305174734420 . 10800001 11600001 51,160,44 -chr2L 11600001 12300001 ID_0.01_17 -0.941807294590 . 11600001 12300001 31,120,180 -chr2L 12300001 12650001 ID_0.01_18 -0.124089226194 . 12300001 12650001 51,160,44 -chr2L 12650001 13150001 ID_0.01_19 -0.535969778416 . 12650001 13150001 31,120,180 -chr2L 13150001 13800001 ID_0.01_20 -0.246694822549 . 13150001 13800001 51,160,44 -chr2L 13800001 14200001 ID_0.01_21 -0.220174816848 . 13800001 14200001 31,120,180 -chr2L 14200001 15650001 ID_0.01_22 -0.512329343230 . 14200001 15650001 51,160,44 -chr2L 15650001 16250001 ID_0.01_23 -0.711741883911 . 15650001 16250001 31,120,180 -chr2L 16250001 17550001 ID_0.01_24 -0.917923384534 . 16250001 17550001 51,160,44 -chr2L 17550001 17850001 ID_0.01_25 -0.423222465610 . 17550001 17850001 31,120,180 -chr2L 17850001 18550001 ID_0.01_26 -0.274143371604 . 17850001 18550001 51,160,44 \ No newline at end of file
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:21:43 2023 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Mon Jul 01 19:55:26 2024 +0000 @@ -1,5 +1,5 @@ -# HiCExplorer hicValidateLocations 3.7.2 -# Overlap of loop file /tmp/tmpjjk1hb59/files/a/8/9/dataset_a8916559-7d4d-42e7-b157-fdc26b57c5e2.dat with protein file /tmp/tmpjjk1hb59/files/e/5/a/dataset_e5ab267d-b489-4abc-88ce-c408eadfd25b.dat +# HiCExplorer hicValidateLocations 3.7.5 +# Overlap of loop file /tmp/tmpjkr0wi60/files/a/f/1/dataset_af1f91e3-b1bd-4c1c-8842-935caae86bf2.dat with protein file /tmp/tmpjkr0wi60/files/e/6/e/dataset_e6e4503d-c6a1-4370-bc34-70b2fae3fc95.dat # Protein peaks: 3097 Matched Loops: 530