# HG changeset patch
# User bgruening
# Date 1509635427 14400
# Node ID ecf11dda45f73fed67cfd19ba1003323454328d3
# Parent 1e0d8c6b3483451449f925d9aeefdf6f1a27b432
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
diff -r 1e0d8c6b3483 -r ecf11dda45f7 _hicExport._xml
--- a/_hicExport._xml Mon Apr 03 07:06:43 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
- saves a HiC Matrix in text format
-
- hicExport
- macros.xml
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 hicCorrectMatrix.xml
--- a/hicCorrectMatrix.xml Mon Apr 03 07:06:43 2017 -0400
+++ b/hicCorrectMatrix.xml Thu Nov 02 11:10:27 2017 -0400
@@ -5,8 +5,8 @@
macros.xml
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@@ -118,7 +120,7 @@
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@@ -129,7 +131,7 @@
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@@ -144,18 +146,16 @@
**What it does**
-Runs Dekker's iterative correction over a hic matrix.
+Runs Dekker's iterative correction over a Hi-C matrix.
+correct: Run the iterative correction.
- correct Run the iterative correction.
- diagnostic_plot
- Plots a histogram of the coverage per bin together with the
- modified z-score based on the median absolute deviation
- method (see Boris Iglewicz and David Hoaglin 1993, Volume
- 16: How to Detect and Handle Outliers The ASQC Basic
- References in Quality Control: Statistical Techniques,
- Edward F. Mykytka, Ph.D., Editor.
-
+diagnostic_plot: Plots a histogram of the coverage per bin together with the
+modified z-score based on the median absolute deviation
+method (see Boris Iglewicz and David Hoaglin 1993, Volume
+16: How to Detect and Handle Outliers The ASQC Basic
+References in Quality Control: Statistical Techniques,
+Edward F. Mykytka, Ph.D., Editor.
]]>
diff -r 1e0d8c6b3483 -r ecf11dda45f7 hicFindEnrichedContacts.xml
diff -r 1e0d8c6b3483 -r ecf11dda45f7 macros.xml
--- a/macros.xml Mon Apr 03 07:06:43 2017 -0400
+++ b/macros.xml Thu Nov 02 11:10:27 2017 -0400
@@ -1,24 +1,11 @@
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- --numberOfProcessors "\${GALAXY_SLOTS:-4}"
- 1.7.2
+ \${GALAXY_SLOTS:-4}
+ 1.8
- python
hicexplorer
-
@BINARY@ --version
@@ -325,7 +312,7 @@
.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _help site: https://github.com/fidelram/deepTools/wiki/
+.. _help site: https://hicexplorer.readthedocs.org
@@ -537,6 +524,33 @@
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/bedgraph_chrx_2e6_5e6.bg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bedgraph_chrx_2e6_5e6.bg Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,11308 @@
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/bigwig_chrx_2e6_5e6.bw
Binary file test-data/bigwig_chrx_2e6_5e6.bw has changed
diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_domains.bed
diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiBonferroni_tad_score.bm Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,23830 @@
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiBonferroni_zscore_matrix.h5
Binary file test-data/find_TADs/multiBonferroni_zscore_matrix.h5 has changed
diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_boundaries.bed Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,2 @@
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_boundaries.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_boundaries.gff Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,2 @@
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_domains.bed
diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiFDR_tad_score.bm Thu Nov 02 11:10:27 2017 -0400
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiFDR_zscore_matrix.h5
Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed
diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_boundaries.bed Thu Nov 02 11:10:27 2017 -0400
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_boundaries.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_boundaries.gff Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,1408 @@
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+chr3L HiCExplorer boundary 14062500 14067500 -0.08770825 . . ID=B02823;delta=0.0361326578947;pvalue=0.577642427572;tad_sep=-0.08770825
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_domains.bed Thu Nov 02 11:10:27 2017 -0400
@@ -0,0 +1,1403 @@
+chr3L 165000 260000 ID_0.01_1 -0.10316675 . 165000 260000 31,120,180
+chr3L 260000 335000 ID_0.01_2 -0.026655 . 260000 335000 51,160,44
+chr3L 335000 360000 ID_0.01_3 -0.030848 . 335000 360000 31,120,180
+chr3L 360000 485000 ID_0.01_4 -0.0580815 . 360000 485000 51,160,44
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+chr3L 525000 680000 ID_0.01_6 -0.1060405 . 525000 680000 51,160,44
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+chr3L 705000 740000 ID_0.01_8 0.002784 . 705000 740000 51,160,44
+chr3L 740000 870000 ID_0.01_9 0.00949975 . 740000 870000 31,120,180
+chr3L 870000 1010000 ID_0.01_10 -0.09546975 . 870000 1010000 51,160,44
+chr3L 1010000 1040000 ID_0.01_11 -0.05182175 . 1010000 1040000 31,120,180
+chr3L 1040000 1110000 ID_0.01_12 -0.05874875 . 1040000 1110000 51,160,44
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 1e0d8c6b3483 -r ecf11dda45f7 test-data/find_TADs/multiNone_tad_score.bm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_tad_score.bm Thu Nov 02 11:10:27 2017 -0400
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