| Next changeset 1:3615a7c5c119 (2017-04-03) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04 |
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added:
_hicExport._xml hicFindEnrichedContacts.xml hicPlotTADs.xml involucro macros.xml test-data/Li_et_al_2015.h5 test-data/diagnostic_plot.png test-data/dm3_genes.bed.gz test-data/dm3_genes.bed6.gz test-data/domains.bed test-data/hicBuildMatrix_result1.bam test-data/hicBuildMatrix_result1.h5 test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicFindTADs_TAD_score.tabular test-data/hicFindTADs_find_boundaries.bed test-data/hicFindTADs_find_boundaries.gff test-data/hicFindTADs_find_domains.bed test-data/hicFindTADs_find_score.bedgraph test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotMatrix_result1.svg test-data/hicPlotTADs_result1.svg test-data/hicSumMatrices_result1.npz.h5 test-data/merged_matrix.npz.h5 test-data/small_test_R1_unsorted.bam test-data/small_test_R2_unsorted.bam test-data/small_test_matrix_50kb_res.h5 test-data/tadScoreFile.tabular_zscore_matrix.h5 test-data/tad_classification.bed test-data/tad_score.gz |
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| diff -r 000000000000 -r 5e0a39c5bcf6 _hicExport._xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_hicExport._xml Thu Mar 30 02:59:24 2017 -0400 |
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| @@ -0,0 +1,55 @@ +<tool id="hicExport" name="hicExport" version="1.0"> + <description>saves a HiC Matrix in text format</description> + <macros> + <token name="@BINARY@">hicExport</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ + hicExport + #if $matrix and $matrix is not None: + --matrix $matrix + #end if + --outputFormat $outputFormat + $clearMaskedBins + --outFileName $output + + ]]></command> + <inputs> + <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" /> + <param label="Output format" name="outputFormat" type="select" + help="There are two possibilities: "dekker" and "ren". + The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels. + The "ren" format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)"> + <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option> + <option value="ren">Ren (chrom, bin_star, bin_end, values)</option> + </param> + <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix" + help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" /> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="matrix" value="hicBuildMatrix_result1.npz"/> + <param name="outputFormat" value="dekker"/> + <output name="output" file="hicExport_result1.txt" ftpye="txt"/> + </test> + <test> + <param name="matrix" value="hicBuildMatrix_result1.npz"/> + <param name="outputFormat" value="ren"/> + <param name="clearMaskedBins" value="True"/> + <output name="output" file="hicExport_result2.txt" ftpye="txt"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Saves a HiC Matrix in text format + + ]]></help> + <expand macro="citations" /> +</tool> + |
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| diff -r 000000000000 -r 5e0a39c5bcf6 hicPlotTADs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicPlotTADs.xml Thu Mar 30 02:59:24 2017 -0400 |
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| b'@@ -0,0 +1,307 @@\n+<tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n+ <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>\n+ <macros>\n+ <token name="@BINARY@">hicPlotTADs</token>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="aggressive">\n+<![CDATA[\n+ sed \'/^$/d\' \'$tracks_config\' &&\n+\n+ @BINARY@\n+ --tracks \'$tracks_config\'\n+ #if $region and $region is not None:\n+ --region \'$region\'\n+ #end if\n+ --outFileName plot.svg\n+\n+]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="tracks_config">\n+## lines that start with \'#\' are comment lines\n+## and are not interpreted by the program\n+## the different tracks are represented by sections in this file\n+## each section starts with a header of the form [hic]\n+## the content of the section label (in the previous example \'hic\') is irrelevant for\n+## plotting and only used to tell the user when something goes wrong.\n+## There are two exceptions for this, the [x-axis] and the [spacer] sections\n+## that use the secion label to determine the action.\n+\n+#if $x_axis.x_axis_select == "yes":\n+[x-axis]\n+fontsize = $x_axis.fontsize\n+where = $x_axis.where\n+#else:\n+[x-axis]\n+#end if\n+\n+#for $counter, $track in enumerate($tracks):\n+[hic_section_$counter]\n+\n+file = $track.track_input\n+\n+#if $track.title\n+title = $track.title\n+#end if\n+\n+#if $track.colormap and $track.track_input.ext == "h5":\n+colormap = $track.colormap\n+#end if\n+\n+#if $track.color and $track.track_input.ext != "h5":\n+color = $track.color\n+#end if\n+\n+#if $track.depth:\n+depth = $track.depth\n+#end if\n+\n+#if $track.display:\n+display = $track.display\n+#end if\n+\n+##color = black\n+\n+#if $track.width\n+width = $track.width\n+#end if\n+\n+#if $track.min_value:\n+# auto is possible\n+min_value = $track.min_value\n+#end if\n+\n+#if $track.max_value:\n+max_value = $track.max_value\n+#end if\n+\n+#if $track.transform\n+transform = $track.transform\n+#end if\n+\n+#if $track.boundaries_file:\n+boundaries_file = $track.boundaries_file\n+#end if\n+\n+#if $track.x_labels == \'yes\':\n+x labels = yes\n+#end if\n+\n+#if $track.track_input.ext == "bedgraph":\n+#set $columns = len(open(str($track.track_input)).readline().split(\'\\t\'))\n+#if $columns > 5:\n+file_type = bedgraph_matrix\n+#else:\n+file_type = bedgraph\n+#end if\n+#elif $track.track_input.ext == "h5":\n+file_type = hic_matrix\n+#else\n+file_type = $track.track_input.ext\n+#end if\n+\n+## show masked bins plots as white lines\n+## those bins that were not used during the correction\n+## the default is to extend neighboring bins to\n+## obtain an aesthetically pleasant output\n+#if $track.show_masked_bins:\n+show_masked_bins = $track.show_masked_bins\n+#end if\n+\n+#if $track.show_data_range:\n+show data range = $track.show_data_range\n+#end if\n+\n+#if $track.nans_to_zeros:\n+nans to zeros = $track.nans_to_zeros\n+#end if\n+\n+## to turn off/on printing of labels\n+#if str($track.labels) == \'off\'\n+labels = off\n+#end if\n+\n+#if $track.global_max_row == \'yes\':\n+global max row = yes\n+#end if\n+\n+## optional: font size can be given if default are not good\n+#if $track.fontsize:\n+fontsize = $track.fontsize\n+#end if\n+\n+#if $track.number_of_bins:\n+number of bins = $track.number_of_bins\n+#end if\n+\n+#if $track.orientation\n+orientation = $track.orientation\n+#end if\n+\n+#if $track.type\n+type = $track.type\n+#end if\n+\n+#if $track.gene_rows\n+gene rows = $track.gene_rows\n+#end if\n+\n+#if $track.spacer_width:\n+[spacer]\n+width = $track.spacer_width\n+#end if\n+\n+\n+#end for</configfile>\n+ </configfiles>\n+ <inputs>\n+ <expand macro="region" />\n+ <repeat name="tracks" min="1" title="Include tracks in your plot"\n+ help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">\n+\n+ <param name="track_input" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track fil'..b'lude spacer at the end of the track." help="Width of the spacer." />\n+\n+ </repeat>\n+\n+ <conditional name="x_axis">\n+ <param name="x_axis_select" type="select" label="Configure x-axis">\n+ <option value="no" selected="True">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="yes">\n+ <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n+ <param name="where" type="select" optional="True" label="Where to place the x-axis">\n+ <option value="top">Top</option>\n+ <option value="bottom">Bottom</option>\n+ </param>\n+ </when>\n+ <when value="no" />\n+ </conditional>\n+\n+ </inputs>\n+ <outputs>\n+ <data name="outFileName" from_work_dir="plot.svg" format="svg"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="region" value="chrX:3000000-3500000"/>\n+ <repeat name="tracks">\n+ <param name="track_input" value="Li_et_al_2015.h5" ftype="h5" />\n+ <param name="title" value="Kc DpnII (Li et al. 2015)"/>\n+ <param name="colormap" value="RdYlBu_r"/>\n+ <param name="depth" value="200000"/>\n+ <param name="transform" value="log1p"/>\n+ <param name="boundaries_file" value="domains.bed"/>\n+ <param name="spacer_width" value="0.5"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="tad_classification.bed" ftype="bed" />\n+ <param name="title" value="TAD state"/>\n+ <param name="width" value="0.5"/>\n+ <param name="display" value="collapsed"/>\n+ <param name="labels" value="off"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="tad_score.gz" ftype="bedgraph" />\n+ <param name="title" value="TAD separation score (Ramirez et al.)"/>\n+ <param name="width" value="10"/>\n+ <param name="type" value="lines"/>\n+ <param name="spacer_width" value="1"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="genes"/>\n+ <param name="width" value="5"/>\n+ <param name="fontsize" value="10"/>\n+ <param name="spacer_width" value="1"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" />\n+ <param name="title" value="max num rows 3"/>\n+ <param name="width" value="3"/>\n+ <param name="fontsize" value="8"/>\n+ <param name="gene_rows" value="3"/>\n+ <param name="spacer_width" value="1"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="dm3_genes.bed6.gz" ftype="bed" />\n+ <param name="title" value="bed6 global max row"/>\n+ <param name="width" value="20"/>\n+ <param name="fontsize" value="10"/>\n+ <param name="global_max_row" value="True"/>\n+ </repeat>\n+ <repeat name="tracks">\n+ <param name="track_input" value="domains.bed" ftype="bed" />\n+ <param name="type" value="vlines"/>\n+ </repeat>\n+ <output name="outFileName" file="hicPlotTADs_result1.svg" ftype="svg" compare="sim_size" delta="35000"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**What it does**\n+\n+Plots the diagonal, and some values close to the diagonal of a HiC matrix. The diagonal of the matrix is plotted horizontally for a region.\n+\n+]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 5e0a39c5bcf6 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 30 02:59:24 2017 -0400 |
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| b'@@ -0,0 +1,542 @@\n+<macros>\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ <regex match="EXception:" />\n+ <regex match="Traceback" />\n+ </stdio>\n+ </xml>\n+\n+ <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+ <token name="@WRAPPER_VERSION@">1.7.1</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="2.7.13">python</requirement>\n+ <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n+ <yield />\n+ </requirements>\n+ <expand macro="stdio" />\n+ <version_command>@BINARY@ --version</version_command>\n+ </xml>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.5281/zenodo.159780</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+ <xml name="zMax">\n+ <param argument="--zMax" name="zMax" type="float" optional="true" label="zMax for 3D plot"/> <!-- this should only be enabled when both or 3d is selected for param whatToShow -->\n+ </xml>\n+\n+ <xml name="colormap">\n+ <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="Accent">Accent</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Blues">Blues</option>\n+ <option value="Greys">Greys</option>\n+ <option value="Purples">Purples</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="autumn">autumn</option>\n+ <option value="winter">winter</option>\n+ <option value="hot">hot</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="cool">cool</option>\n+ <option value="seismic">seismic</option>\n+ <option value="terrain">terrain</option>\n+ <option value="ocean">ocean</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="bone">bone</option>\n+ <option value="flag">flag</option>\n+ <option value="prism">prism</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="binary">binary</option>\n+ <option value="pink">pink</option>\n+ <option value="gray">gray</option>\n+ <option value="copper">copper</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="YlGn">YlGn</option'..b'="93260000" />\n+ </conditional>\n+ </xml>\n+\n+ <xml name="image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="missingDataAsZero">\n+ <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"\n+ label ="Treat missing data as zero"\n+ help ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />\n+ </xml>\n+\n+ <xml name="input_save_matrix_values">\n+ <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>\n+ </xml>\n+\n+ <xml name="input_graphic_output_settings">\n+ <conditional name="output" >\n+ <param name="showOutputSettings" type="select" label="Show advanced output settings" >\n+ <option value="no" selected="true">no</option>\n+ <option value="yes">yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <yield />\n+ <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>\n+ <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="input_image_file_format">\n+ <param name="outFileFormat" type="select" label="Image file format">\n+ <option value="png" selected="true">png</option>\n+ <option value="pdf">pdf</option>\n+ <option value="svg">svg</option>\n+ <option value="eps">eps</option>\n+ <option value="emf">emf</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="output_image_file_format">\n+ <data format="png" name="outFileName" label="${tool.name} image">\n+ <change_format>\n+ <when input="output.outFileFormat" value="pdf" format="pdf" />\n+ <when input="output.outFileFormat" value="svg" format="svg" />\n+ <when input="output.outFileFormat" value="eps" format="eps" />\n+ <when input="output.outFileFormat" value="emf" format="emf" />\n+ </change_format>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_save_matrix_values">\n+ <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveMatrix\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="output_graphic_outputs">\n+ <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveData\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">\n+ <filter>\n+ ((\n+ output[\'showOutputSettings\'] == \'yes\' and\n+ output[\'saveSortedRegions\'] is True\n+ ))\n+ </filter>\n+ </data>\n+ </xml>\n+\n+\n+\n+</macros>\n' |
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@@\n+#{"numberOfProcessors":1,"minDepth":20000,"matrix":"matrix.npz.h5","outFileName":"./tadScoreFile.tabular","binsize":5000,"step":100000,"command":"TAD_score","maxDepth":60000,"zscore_matrix":"./tadScoreFile.tabular_zscore_matrix.h5"}\n+chr2RHet\t0\t5000\t0.000000\n+chr2RHet\t5000\t10000\t-0.095120\n+chr2RHet\t10000\t15000\t-0.086382\n+chr2RHet\t15000\t20000\t-0.080500\n+chr2RHet\t20000\t25000\t-0.075802\n+chr2RHet\t25000\t30000\t0.847009\n+chr2RHet\t30000\t35000\t-0.075802\n+chr2RHet\t35000\t40000\t-0.075802\n+chr2RHet\t40000\t45000\t-0.075802\n+chr2RHet\t45000\t50000\t-0.075802\n+chr2RHet\t50000\t55000\t-0.075802\n+chr2RHet\t55000\t60000\t-0.075802\n+chr2RHet\t60000\t65000\t-0.075802\n+chr2RHet\t65000\t70000\t-0.075802\n+chr2RHet\t70000\t75000\t-0.075802\n+chr2RHet\t75000\t80000\t-0.075802\n+chr2RHet\t80000\t85000\t0.580227\n+chr2RHet\t85000\t90000\t0.580227\n+chr2RHet\t90000\t95000\t0.580227\n+chr2RHet\t95000\t100000\t0.339230\n+chr2RHet\t100000\t105000\t0.339230\n+chr2RHet\t105000\t110000\t-0.075802\n+chr2RHet\t110000\t115000\t-0.075802\n+chr2RHet\t115000\t120000\t-0.075802\n+chr2RHet\t120000\t125000\t1.054400\n+chr2RHet\t125000\t130000\t1.054400\n+chr2RHet\t130000\t135000\t-0.075802\n+chr2RHet\t135000\t140000\t-0.075802\n+chr2RHet\t140000\t145000\t0.339230\n+chr2RHet\t145000\t150000\t0.339230\n+chr2RHet\t150000\t155000\t-0.075802\n+chr2RHet\t155000\t160000\t-0.075802\n+chr2RHet\t160000\t165000\t-0.075802\n+chr2RHet\t165000\t170000\t-0.075802\n+chr2RHet\t170000\t175000\t-0.075802\n+chr2RHet\t175000\t180000\t-0.075802\n+chr2RHet\t180000\t185000\t-0.075802\n+chr2RHet\t185000\t190000\t-0.075802\n+chr2RHet\t190000\t195000\t-0.075802\n+chr2RHet\t195000\t200000\t0.328485\n+chr2RHet\t200000\t205000\t1.712156\n+chr2RHet\t205000\t210000\t1.712156\n+chr2RHet\t210000\t215000\t1.712156\n+chr2RHet\t215000\t220000\t1.056126\n+chr2RHet\t220000\t225000\t-0.075802\n+chr2RHet\t225000\t230000\t-0.075802\n+chr2RHet\t230000\t235000\t-0.075802\n+chr2RHet\t235000\t240000\t-0.075802\n+chr2RHet\t240000\t245000\t-0.075802\n+chr2RHet\t245000\t250000\t-0.075802\n+chr2RHet\t250000\t255000\t-0.075802\n+chr2RHet\t255000\t260000\t-0.075802\n+chr2RHet\t260000\t265000\t-0.075802\n+chr2RHet\t265000\t270000\t-0.075802\n+chr2RHet\t270000\t275000\t-0.075802\n+chr2RHet\t275000\t280000\t-0.075802\n+chr2RHet\t280000\t285000\t-0.075802\n+chr2RHet\t285000\t290000\t-0.075802\n+chr2RHet\t290000\t295000\t-0.075802\n+chr2RHet\t295000\t300000\t-0.075802\n+chr2RHet\t300000\t305000\t-0.075802\n+chr2RHet\t305000\t310000\t-0.075802\n+chr2RHet\t310000\t315000\t-0.075802\n+chr2RHet\t315000\t320000\t-0.075802\n+chr2RHet\t320000\t325000\t-0.075802\n+chr2RHet\t325000\t330000\t-0.075802\n+chr2RHet\t330000\t335000\t-0.075802\n+chr2RHet\t335000\t340000\t-0.075802\n+chr2RHet\t340000\t345000\t-0.075802\n+chr2RHet\t345000\t350000\t-0.075802\n+chr2RHet\t350000\t355000\t-0.075802\n+chr2RHet\t355000\t360000\t-0.075802\n+chr2RHet\t360000\t365000\t-0.075802\n+chr2RHet\t365000\t370000\t-0.075802\n+chr2RHet\t370000\t375000\t-0.075802\n+chr2RHet\t375000\t380000\t1.056126\n+chr2RHet\t380000\t385000\t1.056126\n+chr2RHet\t385000\t390000\t1.056126\n+chr2RHet\t390000\t395000\t1.056126\n+chr2RHet\t395000\t400000\t-0.075802\n+chr2RHet\t400000\t405000\t-0.075802\n+chr2RHet\t405000\t410000\t-0.075802\n+chr2RHet\t410000\t415000\t-0.075802\n+chr2RHet\t415000\t420000\t-0.075802\n+chr2RHet\t420000\t425000\t-0.075802\n+chr2RHet\t425000\t430000\t-0.075802\n+chr2RHet\t430000\t435000\t-0.075802\n+chr2RHet\t435000\t440000\t-0.075802\n+chr2RHet\t440000\t445000\t-0.075802\n+chr2RHet\t445000\t450000\t-0.075802\n+chr2RHet\t450000\t455000\t-0.075802\n+chr2RHet\t455000\t460000\t-0.075802\n+chr2RHet\t460000\t465000\t-0.075802\n+chr2RHet\t465000\t470000\t-0.075802\n+chr2RHet\t470000\t475000\t-0.075802\n+chr2RHet\t475000\t480000\t-0.075802\n+chr2RHet\t480000\t485000\t-0.075802\n+chr2RHet\t485000\t490000\t-0.075802\n+chr2RHet\t490000\t495000\t-0.075802\n+chr2RHet\t495000\t500000\t-0.075802\n+chr2RHet\t500000\t505000\t-0.075802\n+chr2RHet\t505000\t510000\t-0.075802\n+chr2RHet\t510000\t515000\t-0.075802\n+chr2RHet\t515000\t520000\t-0.075802\n+chr2RHet\t520000\t525000\t-0.075802\n+chr2RHet\t525000\t530000\t-0.075802\n+chr2RHet\t530000\t535000\t-0.075802\n+chr2RHet\t535000\t540000\t-0.075802\n+chr2RHet\t540000\t545000\t-0.075802\n+chr2RHet\t545000\t550000\t-0.075802\n+chr2RHet\t550000\t555000\t0.848419\n+chr2RHet\t555000\t560000\t1.504449\n+chr'..b'\n+chr3R\t27375000\t27380000\t-0.202334\n+chr3R\t27380000\t27385000\t-0.202334\n+chr3R\t27385000\t27390000\t-0.202334\n+chr3R\t27390000\t27395000\t-0.202334\n+chr3R\t27395000\t27400000\t0.199516\n+chr3R\t27400000\t27405000\t0.726185\n+chr3R\t27405000\t27410000\t1.190531\n+chr3R\t27410000\t27415000\t0.833625\n+chr3R\t27415000\t27420000\t-0.202334\n+chr3R\t27420000\t27425000\t-0.202334\n+chr3R\t27425000\t27430000\t0.368686\n+chr3R\t27430000\t27435000\t0.691346\n+chr3R\t27435000\t27440000\t0.691346\n+chr3R\t27440000\t27445000\t0.430560\n+chr3R\t27445000\t27450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|
| b |
| diff -r 000000000000 -r 5e0a39c5bcf6 test-data/hicFindTADs_find_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicFindTADs_find_score.bedgraph Thu Mar 30 02:59:24 2017 -0400 |
| b |
| b'@@ -0,0 +1,25245 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|
| b |
| diff -r 000000000000 -r 5e0a39c5bcf6 test-data/hicPlotDistVsCounts_result1.png |
| b |
| Binary file test-data/hicPlotDistVsCounts_result1.png has changed |
| b |
| diff -r 000000000000 -r 5e0a39c5bcf6 test-data/hicPlotMatrix_result1.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicPlotMatrix_result1.svg Thu Mar 30 02:59:24 2017 -0400 |
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