Mercurial > repos > bgruening > hicexplorer_hicplotsvl
changeset 11:1602cc5b673c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
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--- a/macros.xml Tue Nov 05 00:02:06 2024 +0000 +++ b/macros.xml Thu Dec 05 18:43:46 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@TOOL_VERSION@">3.7.5</token> + <token name="@TOOL_VERSION@">3.7.6</token> <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> <token name="@USE_RANGE@">
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.5 +# Created with chicQualityControl version 3.7.6 # 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 Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.5 +# Created with chicQualityControl version 3.7.6 # QC report for matrices: 0_matrix.cool 1_matrix.cool #Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
--- a/test-data/hicDetectLoops/loops.bedgraph Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicDetectLoops/loops.bedgraph Thu Dec 05 18:43:46 2024 +0000 @@ -0,0 +1,2 @@ +chr3L 640000 645000 chr3L 645000 650000 0.10258046718611576 +chr2L 18670000 18675000 chr2L 18675000 18680000 0.23000508888575644
--- a/test-data/hicDifferentialTAD/accepted.txt Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.6 # 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 Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.6 # 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 Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph Thu Dec 05 18:43:46 2024 +0000 @@ -1,3 +1,3 @@ -# Created by HiCExplorer hicHyperoptDetectLoops 3.7.3 +# Created by HiCExplorer hicHyperoptDetectLoops 3.7.6 -{'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 +{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 1300000, 'maximumNumberOfLoops': 5, 'oet': 2.8714859798937415, 'p': 0.012586549394837264, 'peakWidth': 8, 'pit': 63.88073951584609, 'pp': 0.06112040451977812, 'proteinFile': '/tmp/tmpgf9pvov_/files/2/9/7/dataset_2978768e-39c0-4648-aa6e-8f81c54806cb.dat', 'resolution': 2, 'threads': 1, 'windowSize': 11} \ No newline at end of file
--- a/test-data/hicInfo/hicInfo_output.txt Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5 +# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6 File: matrix_name.h5 Size: 33,754 Bin_length: 5000
--- a/test-data/hicInterIntraTAD/output.txt Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicInterIntraTAD version 3.7.5 +# Created with HiCExplorer's hicInterIntraTAD version 3.7.6 # 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 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
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--- a/test-data/hicPlotSVL/p_values.txt Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.5 +# Created with HiCExplorer's hicPlotSVL 3.7.6 # 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 Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Thu Dec 05 18:43:46 2024 +0000 @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.5 +# Created with HiCExplorer's hicPlotSVL 3.7.6 # 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 Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicQuickQC/QC.log Thu Dec 05 18:43:46 2024 +0000 @@ -1,5 +1,5 @@ -File /tmp/tmpjkr0wi60/tmp/tmp8o_td4fd.h5 +File /tmp/tmpgf9pvov_/tmp/tmpovrpxt57.h5 Sequenced reads 983 Min rest. site distance 300 Max library insert size 1000
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Nov 05 00:02:06 2024 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Thu Dec 05 18:43:46 2024 +0000 @@ -1,5 +1,5 @@ -# 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 +# HiCExplorer hicValidateLocations 3.7.6 +# Overlap of loop file /tmp/tmpgf9pvov_/files/2/9/c/dataset_29c1b4d3-8569-4405-ac40-08d8d9077d0d.dat with protein file /tmp/tmpgf9pvov_/files/4/8/3/dataset_48318067-0b54-463f-a9a7-9c751f3b7d1a.dat # Protein peaks: 3097 Matched Loops: 530
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_qc_report_micro-c Thu Dec 05 18:43:46 2024 +0000 @@ -0,0 +1,24 @@ + +File matrix.cool +Sequenced reads 983 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Hi-C contacts 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +Low mapping quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +same fragment 85 (28.33) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +Intra short range (< 20kb) 61 (28.37) +Intra long range (>= 20kb) 130 (60.47) +Read pair type: inward pairs 42 (19.53) +Read pair type: outward pairs 66 (30.70) +Read pair type: left pairs 48 (22.33) +Read pair type: right pairs 35 (16.28)