| Previous changeset 4:b55d7936cbe0 (2017-12-16) Next changeset 6:3889ecd44f20 (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:
hicCorrectMatrix.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 b55d7936cbe0 -r 44919af9194b hicCorrectMatrix.xml --- a/hicCorrectMatrix.xml Sat Dec 16 16:35:10 2017 -0500 +++ b/hicCorrectMatrix.xml Sat Dec 30 09:24:06 2017 -0500 |
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| @@ -7,11 +7,9 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$matrix' temp_matrix.npz.h5 && - hicCorrectMatrix $mode.mode_selector - --matrix temp_matrix.npz.h5 + --matrix '$matrix_h5_cooler' ## special: --chromosomes is optional, but if given needs at least one argument #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ]) @@ -22,7 +20,11 @@ #if $mode.mode_selector == 'correct': --iterNum $mode.iterNum - --outFileName corrected_matrix.npz.h5 + #if $mode.outputFormat == 'h5' + --outFileName matrix.h5 + #elif $mode.outputFormat == 'cool' + --outFileName matrix.cool + #end if #if $mode.filterThreshold_low and $mode.filterThreshold_large: --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large @@ -62,9 +64,7 @@ ]]> </command> <inputs> - <param argument="--matrix" name="matrix" type="data" format="h5" - label="Hi-C matrix" /> - + <expand macro='matrix_h5_cooler_macro' /> <conditional name="mode"> <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range"> <option value="diagnostic_plot">Diagnostic plot</option> @@ -97,7 +97,10 @@ <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" /> <expand macro="filterThreshold" /> - + <param name='outputFormat' type='select' label="Output file format"> + <option value='h5'>HiCExplorer format</option> + <option value="cool">cool</option> + </param> </when> </conditional> @@ -111,16 +114,25 @@ </inputs> <outputs> - <data name="outFileName" from_work_dir="corrected_matrix.npz.h5" format="h5"> + <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5"> + <filter>outputFormat == 'h5'</filter> <filter>mode['mode_selector'] == "correct"</filter> + </data> + <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool"> + <filter>outputFormat == 'cool'</filter> + <filter>mode['mode_selector'] == "correct"</filter> + + </data> + <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png"> <filter>mode['mode_selector'] == "diagnostic_plot"</filter> </data> </outputs> <tests> <test> - <param name="matrix" value="small_test_matrix.h5" ftype="h5"/> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> + <param name="mode_selector" value="correct"/> <repeat name="chromosomes"> <param name="chromosome" value="chrUextra"/> @@ -128,10 +140,12 @@ <repeat name="chromosomes"> <param name="chromosome" value="chr3LHet"/> </repeat> - <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> + <param name='outputFormat' value='h5'/> + + <output name="outFileName_h5" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/> </test> <test> - <param name="matrix" ftype="h5" value="small_test_matrix.h5"/> + <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> <param name="mode_selector" value="diagnostic_plot"/> <repeat name="chromosomes"> <param name="chromosome" value="chrUextra"/> @@ -147,12 +161,12 @@ Matrix correction ================== -| ``hicCorrectMatrix`` runs Dekker's iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix, -| it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only -| chromosomes, as scaffolds create problems with matrix correction. Therefore -| we use the chromosome names (1-19, X, Y) here. -| -| **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix. +``hicCorrectMatrix`` runs Dekker's iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix, +it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only +chromosomes, as scaffolds create problems with matrix correction. Therefore +we use the chromosome names (1-19, X, Y) here. + +**Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix. Matrix correction works in two steps: first a histogram containing the sum of contact per bin (row sum) is produced. This plot needs to be inspected to decide the best threshold for removing bins with lower number of reads. The second steps removes the low scoring bins and does the correction. |
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| diff -r b55d7936cbe0 -r 44919af9194b macros.xml --- a/macros.xml Sat Dec 16 16:35:10 2017 -0500 +++ b/macros.xml Sat Dec 30 09:24:06 2017 -0500 |
| [ |
| @@ -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 b55d7936cbe0 -r 44919af9194b test-data/Li_chrX30-35_cool.png |
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| diff -r b55d7936cbe0 -r 44919af9194b test-data/covariance_small_50kb.cool |
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| diff -r b55d7936cbe0 -r 44919af9194b test-data/hicPlotDistVsCounts_result2.png |
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| diff -r b55d7936cbe0 -r 44919af9194b 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 09:24:06 2017 -0500 |
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| b |
| diff -r b55d7936cbe0 -r 44919af9194b 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 09:24:06 2017 -0500 |
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|
| b |
| diff -r b55d7936cbe0 -r 44919af9194b test-data/pca1.bw |
| b |
| Binary file test-data/pca1.bw has changed |
| b |
| diff -r b55d7936cbe0 -r 44919af9194b test-data/pca2.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pca2.bedgraph Sat Dec 30 09:24:06 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 b55d7936cbe0 -r 44919af9194b 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 09:24:06 2017 -0500 |
| b |
| b'@@ -0,0 +1,1000 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| b |
| diff -r b55d7936cbe0 -r 44919af9194b test-data/small_test_matrix_2.h5 |
| b |
| Binary file test-data/small_test_matrix_2.h5 has changed |
| b |
| diff -r b55d7936cbe0 -r 44919af9194b test-data/small_test_matrix_result_sorted.bam |
| b |
| Binary file test-data/small_test_matrix_result_sorted.bam has changed |
