# HG changeset patch
# User iuc
# Date 1509634315 14400
# Node ID 41d4044e1dfed73d4f2559047a41c9000320e4ff
# Parent d23aa018cc962db7dc722bdaf29a675098e06449
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
diff -r d23aa018cc96 -r 41d4044e1dfe _hicExport._xml
--- a/_hicExport._xml Mon Apr 03 06:18:32 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-
- saves a HiC Matrix in text format
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- hicExport
- macros.xml
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diff -r d23aa018cc96 -r 41d4044e1dfe hicBuildMatrix.xml
--- a/hicBuildMatrix.xml Mon Apr 03 06:18:32 2017 -0400
+++ b/hicBuildMatrix.xml Thu Nov 02 10:51:55 2017 -0400
@@ -5,15 +5,12 @@
macros.xml
- samtools
+ samtools
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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 d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
@@ -0,0 +1,11308 @@
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/bigwig_chrx_2e6_5e6.bw
Binary file test-data/bigwig_chrx_2e6_5e6.bw has changed
diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiBonferroni_boundaries.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiBonferroni_score.bedgraph
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiBonferroni_zscore_matrix.h5
Binary file test-data/find_TADs/multiBonferroni_zscore_matrix.h5 has changed
diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
@@ -0,0 +1,2 @@
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
@@ -0,0 +1,2 @@
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiFDR_domains.bed
diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiFDR_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiFDR_zscore_matrix.h5
Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed
diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
@@ -0,0 +1,1408 @@
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+chr3L HiCExplorer boundary 11512500 11517500 -0.1065995 . . ID=B02313;delta=0.0238808552632;pvalue=0.821431387661;tad_sep=-0.1065995
+chr3L HiCExplorer boundary 11622500 11627500 -0.090991 . . ID=B02335;delta=0.0561489342105;pvalue=0.915478761369;tad_sep=-0.090991
+chr3L HiCExplorer boundary 11712500 11717500 -0.0141535 . . ID=B02353;delta=0.0242261973684;pvalue=0.661411320743;tad_sep=-0.0141535
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+chr3L HiCExplorer boundary 11822500 11827500 -0.0614325 . . ID=B02375;delta=0.0451161315789;pvalue=0.585402048452;tad_sep=-0.0614325
+chr3L HiCExplorer boundary 11927500 11932500 -0.041385 . . ID=B02396;delta=0.0550728289474;pvalue=0.62040533358;tad_sep=-0.041385
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+chr3L HiCExplorer boundary 11977500 11982500 -0.0250355 . . ID=B02406;delta=0.0126468157895;pvalue=0.771747226156;tad_sep=-0.0250355
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 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
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+chr3L 705000 740000 ID_0.01_8 0.002784 . 705000 740000 51,160,44
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diff -r d23aa018cc96 -r 41d4044e1dfe test-data/find_TADs/multiNone_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_TADs/multiNone_score.bedgraph Thu Nov 02 10:51:55 2017 -0400
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diff -r d23aa018cc96 -r 41d4044e1dfe 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 10:51:55 2017 -0400
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