| Previous changeset 2:cdff00acac0f (2017-12-16) Next changeset 4:8cad169bde4c (2018-01-02) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5 |
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modified:
hicMergeMatrixBins.xml macros.xml test-data/hicPlotDistVsCounts_result2.png test-data/small_test_matrix_result_sorted.bam |
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added:
test-data/Li_chrX30-35_cool.png test-data/Li_et_al_2015.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/li_32-33mb_interactions.bedgraph test-data/li_32mb_interactions.bedgraph test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/obs_exp_small_50kb.cool test-data/obs_exp_small_50kb.h5 test-data/pca1.bedgraph test-data/pca1.bw test-data/pca2.bedgraph test-data/pca2.bw test-data/pearson_small_50kb.cool test-data/pearson_small_50kb.h5 test-data/small_matrix_50kb_pearson_pca1_plot.png test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_R1_unsorted.sam test-data/small_test_R2_unsorted.sam test-data/small_test_matrix_2.h5 |
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| diff -r cdff00acac0f -r 5186eda61ca4 hicMergeMatrixBins.xml --- a/hicMergeMatrixBins.xml Sat Dec 16 16:33:36 2017 -0500 +++ b/hicMergeMatrixBins.xml Sat Dec 30 09:16:29 2017 -0500 |
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| @@ -6,11 +6,8 @@ </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - - ln -s '$matrix' input.npz.h5 && - hicMergeMatrixBins - --matrix input.npz.h5 + --matrix '$matrix_h5_cooler' --numBins $numBins $runningWindow --outFileName ./out.npz.h5 @@ -18,7 +15,8 @@ ]]> </command> <inputs> - <param argument="--matrix" type="data" format="h5" label="Matrix to reduce" /> + <expand macro='matrix_h5_cooler_macro' /> + <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" /> </inputs> @@ -27,7 +25,7 @@ </outputs> <tests> <test> - <param name="matrix" value="small_test_matrix.h5" /> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> <param name="numBins" value="5" /> <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" /> </test> @@ -44,7 +42,10 @@ 100 kb * 10 = 1000 kb = 1 Mb -This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it difficult to interpret, especially if the read depth of the Hi-C data is not high. +This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is +to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but +to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it +difficult to interpret, especially if the read depth of the Hi-C data is not high. Input ----- |
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| diff -r cdff00acac0f -r 5186eda61ca4 macros.xml --- a/macros.xml Sat Dec 16 16:33:36 2017 -0500 +++ b/macros.xml Sat Dec 30 09:16:29 2017 -0500 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">1.8.1</token> + <token name="@WRAPPER_VERSION@">2.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement> @@ -11,7 +11,7 @@ <xml name="citations"> <citations> - <citation type="doi">10.5281/zenodo.159780</citation> + <citation type="doi">10.5281/zenodo.1123667</citation> <yield /> </citations> </xml> @@ -166,7 +166,7 @@ <xml name="multiple_input_matrices"> <repeat name="input_files" title="HiC Matrix files" min="2"> - <param name="matrix" type="data" format="h5" + <param name="matrix" type="data" format="h5,cool" label="HiC Matrix file" help=""/> <param name="mlabel" type="text" size="30" optional="true" value="" @@ -179,8 +179,8 @@ #set $matrices = [] #set $mlabels = [] #for $counter, $i in enumerate($input_files): - ln -s $i.matrix #echo str($counter)+'.npz.h5'#; - #silent $matrices.append( '%s.npz.h5' % $counter ) + ln -s $i.matrix #echo str($counter)+'_matrix'#; + #silent $matrices.append( '%s_matrix' % $counter ) #if str($i.mlabel.value) != "": #set $mlabels += ['"%s"' % ($i.mlabel.value)] @@ -299,7 +299,15 @@ <xml name="pseudocount"> <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> </xml> - + <xml name='matrix_h5_cooler_macro'> + <param name='matrix_h5_cooler' type="data" format="h5,cool" + label="Matrix to compute on."/> + + </xml> + <xml name='matrix_h5_cooler_multiple_macro'> + <param name='matrix_h5_cooler_multiple' type="data" format="h5,cool" + label="Matrix to compute on." multiple="True"/> + </xml> <token name="@REFERENCES@"> .. class:: infomark @@ -525,7 +533,7 @@ </xml> <xml name="track_input_h5_macro"> - <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/> + <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/> </xml> <xml name="track_input_bed_macro"> <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/> |
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| diff -r cdff00acac0f -r 5186eda61ca4 test-data/hicPlotDistVsCounts_result2.png |
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| diff -r cdff00acac0f -r 5186eda61ca4 test-data/li_32-33mb_interactions.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/li_32-33mb_interactions.bedgraph Sat Dec 30 09:16:29 2017 -0500 |
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| diff -r cdff00acac0f -r 5186eda61ca4 test-data/li_32mb_interactions.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/li_32mb_interactions.bedgraph Sat Dec 30 09:16:29 2017 -0500 |
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|
| b |
| diff -r cdff00acac0f -r 5186eda61ca4 test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r cdff00acac0f -r 5186eda61ca4 test-data/pca2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca2.bedgraph Sat Dec 30 09:16:29 2017 -0500 |
| b |
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:Z:22\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6008:2166\t0\tchr3R\t7743490\t41\t50M\t*\t0\t0\tGACGGTCAGTCCGAGAAGCATCTGGAGCCGATGGCCAGTTTCNNNNNGCG\t@@@FFDDDHAHFFFHIJIGIJEIGGGGGHGHIHIFGHJEHDI########\tAS:i:77\tXN:i:0\tXM:i:6\tXO:i:0\tXG:i:0\tNM:i:6\tMD:Z:16G25G0G0G0G0C3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6164:2167\t0\tchrU\t1886379\t2\t14S36M\t*\t0\t0\tCGCATTTGAAAGCTAGCTTTCTAGTTTCACTTGTTTGTTTTTNNNNGTTT\tB@CFFFFFHHHHGJHIIIJJJJIJIIJJJJIJIIIJIGIJJJ########\tAS:i:60\tXS:i:56\tXN:i:0\tXM:i:4\tXO:i:0\tXG:i:0\tNM:i:4\tMD:Z:28T0T0T0T4\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6028:2168\t16\tchr3L\t23880171\t0\t27S23M\t*\t0\t0\tAGGAANNNGGACACTATCGAAAAAGCTAGCTTGCAAAGTTCAAATGACCG\t?B800###IIHC<GGFCIHIJJJJJJIJJJJJIJJIIHHGHGFFFDB@@B\tAS:i:46\tXS:i:46\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:23\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2172\t0\tchr3L\t20041224\t44\t50M\t*\t0\t0\tCGAGGAAGCTGCAAATGGTACGGAGCTGCTGGCTGAGGACGTGTTTGTTG\t@@@BDDDDDFDDF9ABGH<CFFHHHGIIIIGIDEG@F)?FG6B8BB;B@@\tAS:i:96\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:37T12\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6218:2174\t16\tchr2R\t19978961\t44\t50M\t*\t0\t0\tAGGAGCGTTCGTACAAGCGAAGCTCGCCGGAGGACGACAAGCTGAGGCGC\t3>9;AEEE?G@=@@@/A:=<BDDGIFC:AGIGFCGHBDDFHDDDDDD@@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6240:2175\t16\tchr2L\t8736543\t42\t50M\t*\t0\t0\tTTAAGTGGACTTCGTTAATGTTTTAAATTTGAAGAATATTTTACGAGTTA\tHIGIHEHFBGIIFJJJIGGJJIJJIJJJJJIIIJIJJHHHHHDFFFFB@@\tAS:i:85\tXN:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tNM:i:2\tMD:Z:4A25C19\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6080:2181\t0\tchr2L\t22737721\t44\t1S49M\t*\t0\t0\tACTCAGTATATATTAAAAGTTTGTTTATACAATATCCTTTTAATAGGTAT\t<@@FFFDDHAHHHJJIEGICHHGFHHEIJJJIIJJJJJIJJGIJIII?FI\tAS:i:98\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:49\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6184:2183\t16\tchr2L\t1627623\t44\t50M\t*\t0\t0\tTTTAGTTATTGGGCTTTAAAAAAATCTAAATTCTGTCATGATTGATTCTG\tJJJJJJIGIIIIIIJIJJJJJJJJJJJJJJIIJIJIJHHHHHFFFFFBCC\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6206:2186\t16\tchr3R\t5530104\t44\t50M\t*\t0\t0\tCACGACGGGACGCCCTAACGGTATCGTGTGTAATTGCAGTTGCACAAGCA\t<@GHCBJIHBJIJJJJJHIJJJIJJJJIGJIIIIGIGHHHGGFDFFFC@@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6022:2190\t0\tchr3R\t17305312\t36\t40M10S\t*\t0\t0\tACTATAGAAATCTATTAAAAGTATTCCATGTAAGCTAGCTTCTCCACTGT\t?@@BDDDFG?HHHEHIIIIIIHHIIIIFIGIIIIIIIIIGDDHGFFHDGD\tAS:i:72\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:36T3\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6130:2190\t0\tchr2R\t13131924\t36\t36M14S\t*\t0\t0\tATATTGAATTCGAGTCAGAAAAAATAAAACGAAGCTAGCTTATCTGTCAT\tCCCFFDFFGGGHDHHGEIHIIJEIJJJJIJJGIJJJJJJJJJJJJIIIJJ\tAS:i:72\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:36\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6163:2192\t16\tchr2L\t7371337\t2\t26M24S\t*\t0\t0\tGGGTTCTCCACCAGCCGGCAAAAGCTAGCTTAAATTAACTTTTAGTTTTA\tFB)B;B=HD9JJJJIJJJJJJJJJJJJJJJJJJJJJHFHHGHFFFFFCCC\tAS:i:52\tXS:i:48\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:26\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6060:2193\t16\tchr3R\t9331177\t44\t50M\t*\t0\t0\tGCTTACTCCTTTGCAGCACTAGTACTAATTTTTTATTTTTTCGAATTTTC\tGGHFCHFGGIJJIGIIHGIIEFGDIJJJIJJJJJIJIHHHHHFFFFFCC@\tAS:i:100\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:50\tYT:Z:UU\n+HWI-ST1180:36:C0TU1ACXX:1:1101:6038:2194\t0\tchrYHet\t283249\t2\t17S33M\t*\t0\t0\tAGGCAGTAAGGCAGTAAGCTAGCTTGCTATGGTATTTTTCCTTAAGTTCC\t@@@DDDDDHHHHHIIGIDC<<EEHICG@?<C>11?ECG<CCDHAAAFFGE\tAS:i:66\tXS:i:60\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:33\tYT:Z:UU\n' |
| b |
| diff -r cdff00acac0f -r 5186eda61ca4 test-data/small_test_R2_unsorted.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_test_R2_unsorted.sam Sat Dec 30 09:16:29 2017 -0500 |
| b |
| b'@@ -0,0 +1,1000 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| b |
| diff -r cdff00acac0f -r 5186eda61ca4 test-data/small_test_matrix_2.h5 |
| b |
| Binary file test-data/small_test_matrix_2.h5 has changed |
| b |
| diff -r cdff00acac0f -r 5186eda61ca4 test-data/small_test_matrix_result_sorted.bam |
| b |
| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
