Mercurial > repos > bgruening > hicexplorer_chicviewpoint

changeset 11:37125838e360 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d
author iuc
date Thu, 05 Dec 2024 18:36:21 +0000
parents c4ed35f4f77f
children
files chicViewpoint.xml macros.xml test-data/cHi-C/chicExportData/aggregate.tar.gz test-data/cHi-C/chicQualityControl/histogram.png test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report test-data/cHi-C/chicQualityControl/sparsity.png test-data/cHi-C/plots.tar.gz test-data/hicAggregateContacts_results1.png test-data/hicAverageRegions/result_rangeInBins_100.npz test-data/hicAverageRegions/result_range_100000.npz test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png test-data/hicCompartmentsPolarization/output_matrix.npz test-data/hicConvertFormat/small_test_matrix_chr4.homer test-data/hicCorrectMatrix/diagnostic_plot.png test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicDetectLoops/loops.bedgraph test-data/hicDifferentialTAD/accepted.txt test-data/hicDifferentialTAD/rejected.txt test-data/hicHyperoptDetectLoops/loops.bedgraph test-data/hicInfo/hicInfo_output.txt test-data/hicInterIntraTAD/output.txt test-data/hicInterIntraTAD/plot.png test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf test-data/hicPCA/pca1_test1.bw test-data/hicPCA/pca2_test1.bw test-data/hicPlotAverageRegions/defaults.png test-data/hicPlotAverageRegions/defaults_log.png test-data/hicPlotAverageRegions/defaults_log1p.png test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotMatrix/plot1.png test-data/hicPlotMatrix/plot2.pdf test-data/hicPlotMatrix/plot3_pca.svg test-data/hicPlotSVL/p_values.txt test-data/hicPlotSVL/plot.png test-data/hicPlotSVL/ratios.txt test-data/hicQuickQC/QC.log test-data/hicValidateLocations/overlap_smc3_statistics test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/raw_qc_report_micro-c test-data/small_test_matrix_result_sorted.bam test-data/small_test_matrix_result_sorted_microc.bam
diffstat 46 files changed, 73 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/chicViewpoint.xml	Mon Nov 04 23:54:39 2024 +0000
+++ b/chicViewpoint.xml	Thu Dec 05 18:36:21 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>computes viewpoints with the given reference points and a background model.</description>
     <macros>
         <token name="@BINARY@">chicViewpoint</token>
--- a/macros.xml	Mon Nov 04 23:54:39 2024 +0000
+++ b/macros.xml	Thu Dec 05 18:36:21 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@">
Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed
Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report	Thu Dec 05 18:36:21 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.
 
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
Binary file test-data/cHi-C/plots.tar.gz has changed
Binary file test-data/hicAggregateContacts_results1.png has changed
Binary file test-data/hicAverageRegions/result_rangeInBins_100.npz has changed
Binary file test-data/hicAverageRegions/result_range_100000.npz has changed
Binary file test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png has changed
Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed
Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed
Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed
Binary file test-data/hicCorrelate_heatmap_result1.png has changed
Binary file test-data/hicCorrelate_scatter_result1.png has changed
--- a/test-data/hicDetectLoops/loops.bedgraph	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicDetectLoops/loops.bedgraph	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicInterIntraTAD/output.txt	Thu Dec 05 18:36:21 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
Binary file test-data/hicInterIntraTAD/plot.png has changed
Binary file test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf has changed
Binary file test-data/hicPCA/pca1_test1.bw has changed
Binary file test-data/hicPCA/pca2_test1.bw has changed
Binary file test-data/hicPlotAverageRegions/defaults.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log1p.png has changed
Binary file test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png has changed
Binary file test-data/hicPlotDistVsCounts_result1.png has changed
Binary file test-data/hicPlotDistVsCounts_result2.png has changed
Binary file test-data/hicPlotMatrix/plot1.png has changed
Binary file test-data/hicPlotMatrix/plot2.pdf has changed
--- a/test-data/hicPlotMatrix/plot3_pca.svg	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg	Thu Dec 05 18:36:21 2024 +0000
@@ -6,11 +6,11 @@
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-    <dc:date>2024-02-11T14:04:07.014551</dc:date>
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     <dc:creator>
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-      <dc:title>Matplotlib v3.6.2, https://matplotlib.org/</dc:title>
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      <g id="text_15">
@@ -633,7 +630,7 @@
     <g id="ytick_9">
      <g id="line2d_14">
       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="291.174828" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="291.174828" style="stroke: #000000; stroke-width: 0.8"/>
       </g>
      </g>
      <g id="text_16">
@@ -661,7 +658,7 @@
     <g id="ytick_10">
      <g id="line2d_15">
       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="240.202362" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="240.202362" style="stroke: #000000; stroke-width: 0.8"/>
       </g>
      </g>
      <g id="text_17">
@@ -677,7 +674,7 @@
     <g id="ytick_11">
      <g id="line2d_16">
       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="189.229897" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="189.229897" style="stroke: #000000; stroke-width: 0.8"/>
       </g>
      </g>
      <g id="text_18">
@@ -693,7 +690,7 @@
     <g id="ytick_12">
      <g id="line2d_17">
       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="138.257431" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="138.257431" style="stroke: #000000; stroke-width: 0.8"/>
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       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="87.284966" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="87.284966" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -725,7 +722,7 @@
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       <g>
-       <use xlink:href="#m7b986001a8" x="571.7" y="36.3125" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m290744b4f8" x="571.7" y="36.3125" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -740,7 +737,7 @@
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    <g id="LineCollection_1"/>
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+   <g id="patch_8">
     <path d="M 536.0375 444.092224 
 L 553.86875 444.092224 
 L 571.7 444.092224 
@@ -957,13 +954,13 @@
 L 75.996591 461.675676 
 L 71.4125 461.675676 
 z
-" clip-path="url(#p13ffe222dd)" style="fill: #1f77b4"/>
+" clip-path="url(#p11b451661a)" style="fill: #1f77b4"/>
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    <g id="matplotlib.axis_5">
     <g id="ytick_15">
      <g id="line2d_20">
       <g>
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+       <use xlink:href="#m710e0e6472" x="71.4125" y="525.344717" style="stroke: #000000; stroke-width: 0.8"/>
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@@ -976,7 +973,7 @@
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       <g>
-       <use xlink:href="#m116929dbf3" x="71.4125" y="493.510197" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m710e0e6472" x="71.4125" y="493.510197" style="stroke: #000000; stroke-width: 0.8"/>
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      </g>
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@@ -989,7 +986,7 @@
     <g id="ytick_17">
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       <g>
-       <use xlink:href="#m116929dbf3" x="71.4125" y="461.675676" style="stroke: #000000; stroke-width: 0.8"/>
+       <use xlink:href="#m710e0e6472" x="71.4125" y="461.675676" style="stroke: #000000; stroke-width: 0.8"/>
       </g>
      </g>
      <g id="text_24">
@@ -1004,10 +1001,7 @@
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  </g>
  <defs>
-  <clipPath id="p149ee43c70">
-   <rect x="536.0375" y="36.3125" width="35.6625" height="407.779724"/>
-  </clipPath>
-  <clipPath id="p13ffe222dd">
+  <clipPath id="p11b451661a">
    <rect x="71.4125" y="458.492224" width="453.825" height="70.035945"/>
   </clipPath>
  </defs>
--- a/test-data/hicPlotSVL/p_values.txt	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicPlotSVL/p_values.txt	Thu Dec 05 18:36:21 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
Binary file test-data/hicPlotSVL/plot.png has changed
--- a/test-data/hicPlotSVL/ratios.txt	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicPlotSVL/ratios.txt	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicQuickQC/QC.log	Thu Dec 05 18:36:21 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	Mon Nov 04 23:54:39 2024 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics	Thu Dec 05 18:36:21 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
Binary file test-data/li_viewpoint_32-33Mb.png has changed
Binary file test-data/li_viewpoint_32Mb.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw_qc_report_micro-c	Thu Dec 05 18:36:21 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)
Binary file test-data/small_test_matrix_result_sorted.bam has changed
Binary file test-data/small_test_matrix_result_sorted_microc.bam has changed