# HG changeset patch # User bgruening # Date 1520412362 18000 # Node ID 94fff1a6a8995bb5e7f3d62d9b6edde2605bda71 # Parent 36ef3cb8ae2e51dfb176cb8c626110861702a6c8 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457 diff -r 36ef3cb8ae2e -r 94fff1a6a899 hicPlotTADs.xml --- a/hicPlotTADs.xml Tue Jan 02 10:20:13 2018 -0500 +++ b/hicPlotTADs.xml Wed Mar 07 03:46:02 2018 -0500 @@ -48,6 +48,7 @@ max_value = $track.track_file_style_conditional.max_value #end if transform = $track.track_file_style_conditional.transform +width = $track.track_file_style_conditional.width_matrix #if $track.track_file_style_conditional.boundaries_file: boundaries_file = $track.track_file_style_conditional.boundaries_file #end if @@ -76,6 +77,9 @@ #if $track.track_file_style_conditional.width_tad: width = $track.track_file_style_conditional.width_tad #end if +#if $track.track_file_style_conditional.type_lines: +type = $track.track_file_style_conditional.type_lines +#end if #if $track.track_file_style_conditional.show_data: show data range = $track.track_file_style_conditional.show_data #end if @@ -246,7 +250,7 @@ - + @@ -267,6 +271,8 @@ + + @@ -282,7 +288,9 @@ - + diff -r 36ef3cb8ae2e -r 94fff1a6a899 involucro Binary file involucro has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 macros.xml --- a/macros.xml Tue Jan 02 10:20:13 2018 -0500 +++ b/macros.xml Wed Mar 07 03:46:02 2018 -0500 @@ -1,6 +1,13 @@ \${GALAXY_SLOTS:-4} - 2.0 + 2.1 + + + #if $use_range.select_use_range == "yes_use_range": + --range $range_min:$range_max + #end if + + hicexplorer @@ -19,6 +26,23 @@ + + + + + + + + + + + + + + + + + @@ -300,13 +324,12 @@ - - + - + @@ -556,9 +579,9 @@ + label="Include spacer at the end of the track." help="Width of the spacer." /> - + diff -r 36ef3cb8ae2e -r 94fff1a6a899 macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml.orig Wed Mar 07 03:46:02 2018 -0500 @@ -0,0 +1,585 @@ + + \${GALAXY_SLOTS:-4} +<<<<<<< HEAD + 2.0 + + + #if $use_range.select_use_range == "yes_use_range": + --range $range_min:$range_max + #end if + + +======= + 2.1alpha1 +>>>>>>> joachimwolff-master + + + hicexplorer + + + @BINARY@ --version + + + + + 10.5281/zenodo.1133705 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #set $matrices = [] + #set $mlabels = [] + #for $counter, $i in enumerate($input_files): + 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)] + #else + #set $mlabels += ['"%s"' % ($i.matrix.name)] + #end if + #end for + #set $mlabels = ' '.join($mlabels) + #set $matrices = ' '.join($matrices) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _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://hicexplorer.readthedocs.org + + + + + + + + + + + + + + + + + + + + + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) + #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) + #silent $files.append('%s.bam' % $temp_input_path) + + ##set $files += [str($i.bamfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bamfile.name)] + #end if + #end for + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) + #silent $files.append('%s.bw' % $temp_input_path) + + ##set $files += [str($i.bigwigfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] + #end if + #end for + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "${source.input1_2bit.fields.path}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/Li_chrX30-35_cool.png Binary file test-data/Li_chrX30-35_cool.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/compare_matrices_log2ratio.h5 Binary file test-data/compare_matrices_log2ratio.h5 has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/compare_matrices_pearson_ratio.cool Binary file test-data/compare_matrices_pearson_ratio.cool has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/covariance_small_50kb.cool Binary file test-data/covariance_small_50kb.cool has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/covariance_small_50kb.h5 Binary file test-data/covariance_small_50kb.h5 has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/diagnostic_plot.png Binary file test-data/diagnostic_plot.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicAggregateContacts_results1.png Binary file test-data/hicAggregateContacts_results1.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicCorrectMatrix_result1.npz.h5 Binary file test-data/hicCorrectMatrix_result1.npz.h5 has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicCorrelate_heatmap_result1.png Binary file test-data/hicCorrelate_heatmap_result1.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicCorrelate_scatter_result1.png Binary file test-data/hicCorrelate_scatter_result1.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicMergeMatrixBins_result1.npz.h5 Binary file test-data/hicMergeMatrixBins_result1.npz.h5 has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicPlotDistVsCounts_result1.png Binary file test-data/hicPlotDistVsCounts_result1.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicPlotDistVsCounts_result2.png Binary file test-data/hicPlotDistVsCounts_result2.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/hicSumMatrices_result1.npz.h5 Binary file test-data/hicSumMatrices_result1.npz.h5 has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/li_viewpoint_32-33Mb.png Binary file test-data/li_viewpoint_32-33Mb.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/li_viewpoint_32Mb.png Binary file test-data/li_viewpoint_32Mb.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/master_TADs_plot.png Binary file test-data/master_TADs_plot.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/master_matrix_plot.png Binary file test-data/master_matrix_plot.png has changed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.bed Wed Mar 07 03:46:02 2018 -0500 @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B04585 -0.068256362891 . +chrX 87500 92500 B19358 -0.072020401017 . diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.gff Wed Mar 07 03:46:02 2018 -0500 @@ -0,0 +1,2 @@ +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 36ef3cb8ae2e -r 94fff1a6a899 test-data/multiFDR_domains.bed diff -r 36ef3cb8ae2e -r 94fff1a6a899 test-data/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_score.bedgraph Wed Mar 07 03:46:02 2018 -0500 @@ -0,0 +1,23814 @@ +chr2L 2500 7500 -0.164488846397 +chr2L 7500 12500 0.004155516280 +chr2L 12500 17500 0.260509497302 +chr2L 17500 22500 0.126728724578 +chr2L 22500 27500 0.107536542495 +chr2L 27500 32500 0.067996441287 +chr2L 32500 37500 0.180067325085 +chr2L 37500 42500 0.188704045555 +chr2L 42500 47500 0.123071283383 +chr2L 47500 52500 0.090946822420 +chr2L 52500 57500 0.050290136708 +chr2L 57500 62500 0.043738171585 +chr2L 62500 67500 0.036458137676 +chr2L 67500 72500 -0.008311665224 +chr2L 72500 77500 -0.025506335364 +chr2L 77500 82500 -0.028782499450 +chr2L 82500 87500 -0.008859983289 +chr2L 87500 92500 0.012581289189 +chr2L 92500 97500 -0.026656341295 +chr2L 97500 102500 -0.064470557052 +chr2L 102500 107500 -0.022699733707 +chr2L 107500 112500 -0.026264267296 +chr2L 112500 117500 -0.009926677809 +chr2L 117500 122500 -0.006876513913 +chr2L 122500 127500 0.016147318959 +chr2L 127500 132500 0.022378914981 +chr2L 132500 137500 0.070952047599 +chr2L 137500 142500 0.071053469305 +chr2L 142500 147500 0.068034199638 +chr2L 147500 152500 0.067090397637 +chr2L 152500 157500 0.057311311696 +chr2L 157500 162500 0.067610279560 +chr2L 162500 167500 0.029002777185 +chr2L 167500 172500 0.029002777185 +chr2L 172500 177500 0.008980247068 +chr2L 177500 182500 0.016907224460 +chr2L 182500 187500 -0.000150569937 +chr2L 187500 192500 0.010495785312 +chr2L 192500 197500 -0.048163268016 +chr2L 197500 202500 -0.039867994837 +chr2L 202500 207500 -0.046910414090 +chr2L 207500 212500 -0.055696730183 +chr2L 212500 217500 -0.036501614110 +chr2L 217500 222500 -0.036501614110 +chr2L 222500 227500 -0.023335648652 +chr2L 227500 232500 -0.023335648652 +chr2L 232500 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0.092016050812 +chr2L 372500 377500 0.061075544744 +chr2L 377500 382500 0.013498603323 +chr2L 382500 387500 0.029781933737 +chr2L 387500 392500 -0.021388944213 +chr2L 392500 397500 -0.038792978876 +chr2L 397500 402500 -0.050263472402 +chr2L 402500 407500 -0.044321193230 +chr2L 407500 412500 -0.007732343879 +chr2L 412500 417500 -0.013295314500 +chr2L 417500 422500 -0.013295314500 +chr2L 422500 427500 -0.021132388853 +chr2L 427500 432500 -0.021015012893 +chr2L 432500 437500 -0.015982567418 +chr2L 437500 442500 -0.049145302596 +chr2L 442500 447500 -0.064964420946 +chr2L 447500 452500 -0.051664858126 +chr2L 452500 457500 -0.071914886809 +chr2L 457500 462500 -0.069724393991 +chr2L 462500 467500 -0.069724393991 +chr2L 467500 472500 -0.059605045512 +chr2L 472500 477500 -0.051309772332 +chr2L 477500 482500 -0.048373705573 +chr2L 482500 487500 -0.048373705573 +chr2L 487500 492500 -0.014227247533 +chr2L 492500 497500 -0.064541001831 +chr2L 497500 502500 -0.064541001831 +chr2L 502500 507500 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-0.104690774223 +chr2L 642500 647500 -0.104690774223 +chr2L 647500 652500 -0.053713171413 +chr2L 652500 657500 -0.032383933202 +chr2L 657500 662500 -0.013390883314 +chr2L 662500 667500 -0.023624746219 +chr2L 667500 672500 -0.015426022630 +chr2L 672500 677500 -0.013822637003 +chr2L 677500 682500 -0.013822637003 +chr2L 682500 687500 -0.028847855386 +chr2L 687500 692500 0.017132537265 +chr2L 692500 697500 0.017132537265 +chr2L 697500 702500 0.045710448555 +chr2L 702500 707500 0.027583820124 +chr2L 707500 712500 -0.028547755658 +chr2L 712500 717500 -0.000317643464 +chr2L 717500 722500 -0.014643992043 +chr2L 722500 727500 -0.014643992043 +chr2L 727500 732500 -0.017732383711 +chr2L 732500 737500 0.001546317552 +chr2L 737500 742500 -0.014947679217 +chr2L 742500 747500 -0.007136697412 +chr2L 747500 752500 -0.023340488177 +chr2L 752500 757500 -0.003090459494 +chr2L 757500 762500 -0.002431239390 +chr2L 762500 767500 0.019169021058 +chr2L 767500 772500 0.056276552730 +chr2L 772500 777500 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