Galaxy |

Changeset 10:9c5ffb1f836f (2018-04-27)

Previous changeset 9:653c6fead9f9 (2018-04-27) Next changeset 11:c2521cba1c32 (2018-06-09)

Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dddc0b9035b8edadfd45d74b01aeca245c2725d7

added:
static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png
static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
static/images/hicPlotDistVsCounts.png

diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png

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diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicCompareMatrices_QC_log2_m50_matrix_plot.png

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diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png

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diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png

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diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicPlotDistVsCounts.png

Binary file static/images/hicPlotDistVsCounts.png has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f static/images/hicPlotDistvsCounts.png

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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiBonferroni_boundaries.bed
--- a/test-data/find_TADs/multiBonferroni_boundaries.bed Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L 22922500 22927500 B09504 -0.06825625 .
-chrX 87500 92500 B09542 -0.0720205 .

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiBonferroni_boundaries.gff
--- a/test-data/find_TADs/multiBonferroni_boundaries.gff Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L HiCExplorer boundary 22922500 22927500 -0.06825625 . . ID=B09504;delta=0.0219547105263;pvalue=0.0547512191318;tad_sep=-0.06825625
-chrX HiCExplorer boundary 87500 92500 -0.0720205 . . ID=B09542;delta=0.0197999736842;pvalue=0.0890201733631;tad_sep=-0.0720205

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiBonferroni_score.bedgraph
--- a/test-data/find_TADs/multiBonferroni_score.bedgraph Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23814 +0,0 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n-chr3R\t27417500\t27422500\t-0.0499295\n-chr3R\t27422500\t27427500\t-0.04139125\n-chr3R\t27427500\t27432500\t-0.0366555\n-chr3R\t27432500\t27437500\t-0.0366555\n-chr3R\t27437500\t27442500\t-0.04748775\n-chr3R\t27442500\t27447500\t-0.05511025\n-chr3R\t27447500\t27452500\t-0.05736225\n-chr3R\t27452500\t27457500\t-0.0233205\n-chr3R\t27457500\t27462500\t-0.0020265\n-chr3R\t27462500\t27467500\t0.02501975\n-chr3R\t27467500\t27472500\t0.036331\n-chr3R\t27472500\t27477500\t0.036331\n-chr3R\t27477500\t27482500\t0.036331\n-chr3R\t27482500\t27487500\t0.06726625\n-chr3R\t27487500\t27492500\t0.06726625\n-chr3R\t27492500\t27497500\t0.0926245\n-chr3R\t27497500\t27502500\t0.098145\n-chr3R\t27502500\t27507500\t0.088452\n-chr3R\t27507500\t27512500\t0.0991195\n-chr3R\t27512500\t27517500\t0.07477075\n-chr3R\t27517500\t27522500\t0.07477075\n-chr3R\t27522500\t27527500\t0.07477075\n-chr3R\t27527500\t27532500\t0.07477075\n-chr3R\t27532500\t27537500\t0.07667425\n-chr3R\t27537500\t27542500\t0.08198875\n-chr3R\t27542500\t27547500\t0.068792\n-chr3R\t27547500\t27552500\t0.00660575\n-chr3R\t27552500\t27557500\t-0.06866275\n-chr3R\t27557500\t27562500\t-0.063076\n-chr3R\t27562500\t27567500\t-0.063076\n-chr3R\t27567500\t27572500\t-0.08094325\n-chr3R\t27572500\t27577500\t-0.07177225\n-chr3R\t27577500\t27582500\t0.00014175\n-chr3R\t27582500\t27587500\t-0.004425\n-chr3R\t27587500\t27592500\t-0.0055905\n-chr3R\t27592500\t27597500\t0.0107725\n-chr3R\t27597500\t27602500\t0.012076\n-chr3R\t27602500\t27607500\t0.00204375\n-chr3R\t27607500\t27612500\t0.01391525\n-chr3R\t27612500\t27617500\t0.02616875\n-chr3R\t27617500\t27622500\t0.02862975\n-chr3R\t27622500\t27627500\t0.02862975\n-chr3R\t27627500\t27632500\t0.03521625\n-chr3R\t27632500\t27637500\t0.00040125\n-chr3R\t27637500\t27642500\t0.0303095\n-chr3R\t27642500\t27647500\t0.090842\n-chr3R\t27647500\t27652500\t0.10491025\n-chr3R\t27652500\t27657500\t0.11880175\n-chr3R\t27657500\t27662500\t0.09649925\n-chr3R\t27662500\t27667500\t0.07636225\n-chr3R\t27667500\t27672500\t0.06380525\n-chr3R\t27672500\t27677500\t0.04760175\n-chr3R\t27677500\t27682500\t0.02274975\n-chr3R\t27682500\t27687500\t0.015637\n-chr3R\t27687500\t27692500\t0.015637\n-chr3R\t27692500\t27697500\t0.025063\n-chr3R\t27697500\t27702500\t-0.01535\n-chr3R\t27702500\t27707500\t-0.01535\n-chr3R\t27707500\t27712500\t0.00155075\n-chr3R\t27712500\t27717500\t0.006288\n-chr3R\t27717500\t27722500\t0.006288\n-chr3R\t27722500\t27727500\t-0.00858325\n-chr3R\t27727500\t27732500\t0.02622075\n-chr3R\t27732500\t27737500\t0.097312\n-chr3R\t27737500\t27742500\t0.067952\n-chr3R\t27742500\t27747500\t0.0387865\n-chr3R\t27747500\t27752500\t0.01357725\n-chr3R\t27752500\t27757500\t0.02531675\n-chr3R\t27757500\t27762500\t0.033303\n-chr3R\t27762500\t27767500\t0.050386\n-chr3R\t27767500\t27772500\t0.0229625\n-chr3R\t27772500\t27777500\t0.04058825\n-chr3R\t27777500\t27782500\t0.03747975\n-chr3R\t27782500\t27787500\t0.0294565\n-chr3R\t27787500\t27792500\t0.07453225\n-chr3R\t27792500\t27797500\t0.08362425\n-chr3R\t27797500\t27802500\t0.06882\n-chr3R\t27802500\t27807500\t0.075945\n-chr3R\t27807500\t27812500\t0.11806575\n-chr3R\t27812500\t27817500\t0.152855\n-chr3R\t27817500\t27822500\t0.1721425\n-chr3R\t27822500\t27827500\t0.17090925\n-chr3R\t27827500\t27832500\t0.15466375\n-chr3R\t27832500\t27837500\t0.1765955\n-chr3R\t27837500\t27842500\t0.16170225\n-chr3R\t27842500\t27847500\t0.16431675\n-chr3R\t27847500\t27852500\t0.20353925\n-chr3R\t27852500\t27857500\t0.19259975\n-chr3R\t27857500\t27862500\t0.13903775\n-chr3R\t27862500\t27867500\t0.1658075\n-chr3R\t27867500\t27872500\t0.033584\n-chr3R\t27872500\t27877500\t-0.044813\n-chr3R\t27877500\t27882500\t-0.1079445\n-chr3R\t27882500\t27887500\t-0.1024605\n-chr3R\t27887500\t27892500\t-0.09179375\n-chr3R\t27892500\t27897500\t-0.1533095\n-chr3R\t27897500\t27902500\t-0.15876925\n-chr3R\t27902500\t27905026\t0.0\n-chrUextra\t2500\t29002328\t0.0\n-chrM\t2500\t17258\t0.0\n-chr3LHet\t2500\t2555245\t0.0\n'

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiBonferroni_tad_score.bm
--- a/test-data/find_TADs/multiBonferroni_tad_score.bm Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiBonferroni_zscore_matrix.h5

Binary file test-data/find_TADs/multiBonferroni_zscore_matrix.h5 has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiFDR_zscore_matrix.h5

Binary file test-data/find_TADs/multiFDR_zscore_matrix.h5 has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_boundaries.bed
--- a/test-data/find_TADs/multiNone_boundaries.bed Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1408 +0,0 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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_boundaries.gff
--- a/test-data/find_TADs/multiNone_boundaries.gff Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1408 +0,0 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407500\t-0.00546225\t.\t.\tID=B23322;delta=0.0185628552632;pvalue=0.846835522646;tad_sep=-0.00546225\n-chr3R\tHiCExplorer\tboundary\t25567500\t25572500\t-0.04654075\t.\t.\tID=B23355;delta=0.0566089736842;pvalue=0.576192906383;tad_sep=-0.04654075\n-chr3R\tHiCExplorer\tboundary\t25577500\t25582500\t-0.01871575\t.\t.\tID=B23357;delta=0.0281310394737;pvalue=0.314699364851;tad_sep=-0.01871575\n-chr3R\tHiCExplorer\tboundary\t25727500\t25732500\t-0.00858875\t.\t.\tID=B23387;delta=0.0986943815789;pvalue=0.112031426493;tad_sep=-0.00858875\n-chr3R\tHiCExplorer\tboundary\t25877500\t25882500\t-0.10581625\t.\t.\tID=B23417;delta=0.0288810657895;pvalue=0.48806712443;tad_sep=-0.10581625\n-chr3R\tHiCExplorer\tboundary\t25987500\t25992500\t-0.090403\t.\t.\tID=B23439;delta=0.0182022894737;pvalue=0.952043612098;tad_sep=-0.090403\n-chr3R\tHiCExplorer\tboundary\t26047500\t26052500\t-0.0935315\t.\t.\tID=B23451;delta=0.0351577631579;pvalue=0.420309304718;tad_sep=-0.0935315\n-chr3R\tHiCExplorer\tboundary\t26177500\t26182500\t-0.11469275\t.\t.\tID=B23477;delta=0.0468813947368;pvalue=0.407773352255;tad_sep=-0.11469275\n-chr3R\tHiCExplorer\tboundary\t26272500\t26277500\t-0.1002735\t.\t.\tID=B23496;delta=0.0265311973684;pvalue=0.866273462912;tad_sep=-0.1002735\n-chr3R\tHiCExplorer\tboundary\t26327500\t26332500\t-0.092304\t.\t.\tID=B23507;delta=0.0340349736842;pvalue=0.801678295331;tad_sep=-0.092304\n-chr3R\tHiCExplorer\tboundary\t26487500\t26492500\t0.0627965\t.\t.\tID=B23539;delta=0.0261305394737;pvalue=0.917163037297;tad_sep=0.0627965\n-chr3R\tHiCExplorer\tboundary\t26562500\t26567500\t-0.01974475\t.\t.\tID=B23554;delta=0.0717252631579;pvalue=0.774996850942;tad_sep=-0.01974475\n-chr3R\tHiCExplorer\tboundary\t26637500\t26642500\t-0.07430725\t.\t.\tID=B23569;delta=0.0364784868421;pvalue=0.687771555077;tad_sep=-0.07430725\n-chr3R\tHiCExplorer\tboundary\t26712500\t26717500\t-0.049789\t.\t.\tID=B23584;delta=0.0413630789474;pvalue=0.926151939522;tad_sep=-0.049789\n-chr3R\tHiCExplorer\tboundary\t26867500\t26872500\t-0.0249905\t.\t.\tID=B23615;delta=0.0878640789474;pvalue=0.360644376149;tad_sep=-0.0249905\n-chr3R\tHiCExplorer\tboundary\t27042500\t27047500\t-0.074189\t.\t.\tID=B23650;delta=0.0714735131579;pvalue=0.596640534697;tad_sep=-0.074189\n-chr3R\tHiCExplorer\tboundary\t27152500\t27157500\t-0.00609925\t.\t.\tID=B23672;delta=0.0508306842105;pvalue=0.667062852012;tad_sep=-0.00609925\n-chr3R\tHiCExplorer\tboundary\t27182500\t27187500\t-0.01281025\t.\t.\tID=B23678;delta=0.0210053815789;pvalue=0.481433141582;tad_sep=-0.01281025\n-chr3R\tHiCExplorer\tboundary\t27247500\t27252500\t-0.04990275\t.\t.\tID=B23691;delta=0.0377629210526;pvalue=0.746434392485;tad_sep=-0.04990275\n-chr3R\tHiCExplorer\tboundary\t27382500\t27387500\t-0.041305\t.\t.\tID=B23718;delta=0.0604152368421;pvalue=0.443941047643;tad_sep=-0.041305\n-chr3R\tHiCExplorer\tboundary\t27417500\t27422500\t-0.0499295\t.\t.\tID=B23725;delta=0.040293;pvalue=0.772288553997;tad_sep=-0.0499295\n-chr3R\tHiCExplorer\tboundary\t27567500\t27572500\t-0.08094325\t.\t.\tID=B23755;delta=0.0899101052632;pvalue=0.377997904893;tad_sep=-0.08094325\n-chr3R\tHiCExplorer\tboundary\t27697500\t27702500\t-0.01535\t.\t.\tID=B23781;delta=0.0567128421053;pvalue=0.546627372724;tad_sep=-0.01535\n-chr3R\tHiCExplorer\tboundary\t27747500\t27752500\t0.01357725\t.\t.\tID=B23791;delta=0.0162098684211;pvalue=0.746434392485;tad_sep=0.01357725\n-chr3R\tHiCExplorer\tboundary\t27767500\t27772500\t0.0229625\t.\t.\tID=B23795;delta=0.0310075921053;pvalue=0.767420623706;tad_sep=0.0229625\n'

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_domains.bed
--- a/test-data/find_TADs/multiNone_domains.bed Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,1403 +0,0 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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_score.bedgraph
--- a/test-data/find_TADs/multiNone_score.bedgraph Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_tad_score.bm
--- a/test-data/find_TADs/multiNone_tad_score.bm Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/find_TADs/multiNone_zscore_matrix.h5

Binary file test-data/find_TADs/multiNone_zscore_matrix.h5 has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/hicBuildMatrix_result1.bam

Binary file test-data/hicBuildMatrix_result1.bam has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/merged_matrix.npz.h5

Binary file test-data/merged_matrix.npz.h5 has changed

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/multiFDR_boundaries.bed
--- a/test-data/multiFDR_boundaries.bed Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L 22922500 22927500 B04585 -0.068256362891 .
-chrX 87500 92500 B19358 -0.072020401017 .

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/multiFDR_boundaries.gff
--- a/test-data/multiFDR_boundaries.gff Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-chr2L HiCExplorer boundary 22922500 22927500 -0.068256362891 . . ID=B04585;delta=0.021954846720;pvalue=0.000033964776;tad_sep=-0.068256362891
-chrX HiCExplorer boundary 87500 92500 -0.072020401017 . . ID=B19358;delta=0.019799980104;pvalue=0.000055223433;tad_sep=-0.072020401017

diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/multiFDR_score.bedgraph
--- a/test-data/multiFDR_score.bedgraph Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23814 +0,0 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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/multiFDR_tad_score.bm
--- a/test-data/multiFDR_tad_score.bm Fri Apr 27 03:36:47 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,23830 +0,0 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diff -r 653c6fead9f9 -r 9c5ffb1f836f test-data/small_test_matrix_result.bam

Binary file test-data/small_test_matrix_result.bam has changed