| Previous changeset 7:43332e51a712 (2018-03-07) Next changeset 9:4ce06ae9893a (2018-04-27) |
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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 |
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modified:
hicFindTADs.xml macros.xml test-data/compare_matrices_log2ratio.h5 test-data/compare_matrices_pearson_ratio.cool test-data/covariance_small_50kb.cool test-data/covariance_small_50kb.h5 test-data/hicCorrectMatrix_result1.npz.h5 test-data/hicMergeMatrixBins_result1.npz.h5 test-data/hicPlotDistVsCounts_result2.png test-data/hicSumMatrices_result1.npz.h5 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.bw test-data/pearson_small_50kb.h5 test-data/pearson_small_50kb_transform.cool test-data/small_matrix_50kb_pearson_pca1_plot.svg test-data/small_test_matrix_2.h5 |
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added:
static/images/hicAggregateContacts.png static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png static/images/hicCorrelate_Dmel_heatmap.png static/images/hicCorrelate_Dmel_scatterplot.png static/images/hicMergeMatrixBins_Xchr.png static/images/hicMergeMatrixBins_Xregion.png static/images/hicPCA.png static/images/hicPlotDistvsCounts.png static/images/hicPlotMatrix.png static/images/hicPlotTADs.png static/images/hicQC_distance.png static/images/hicQC_pairs_discarded.png static/images/hicQC_pairs_sequenced.png static/images/hicQC_read_orientation.png static/images/hicQC_unmappable_and_non_unique.png static/images/pulication_plots_viewpoint.png |
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removed:
involucro macros.xml.orig test-data/multiFDR_zscore_matrix.h5 |
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| diff -r 43332e51a712 -r b05f292d220c hicFindTADs.xml --- a/hicFindTADs.xml Wed Mar 07 03:46:54 2018 -0500 +++ b/hicFindTADs.xml Fri Apr 27 03:39:27 2018 -0400 |
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| b'@@ -1,5 +1,5 @@\n <tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n- <description>find minimum cuts that correspond to boundaries</description>\n+ <description>identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin</description>\n <macros>\n <token name="@BINARY@">hicFindTADs</token>\n <import>macros.xml</import>\n@@ -8,7 +8,7 @@\n <command detect_errors="exit_code"><![CDATA[\n hicFindTADs\n --matrix \'$matrix_h5_cooler\'\n- \n+\n --delta $delta\n \n #if $minBoundaryDistance:\n@@ -24,7 +24,7 @@\n --correctForMultipleTesting bonferroni\n --threshold $multiple_comparison_conditional.threshold\n #else:\n- --multipleComparisons None \n+ --multipleComparisons None\n #end if\n \n --numberOfProcessors @THREADS@\n@@ -70,21 +70,21 @@\n \n <param argument="--minBoundaryDistance" type="integer" value="" optional="True"\n label="Minimum distance between boundaries (in bp)."\n- help="This parameter can be used to reduce spurious boundaries caused by noise. "/> \n+ help="This parameter can be used to reduce spurious boundaries caused by noise. "/>\n \n </inputs>\n <outputs>\n- \n+\n <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"\n label="${tool.name} on ${on_string}: Boundary positions" />\n- \n+\n <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"\n label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores" />\n <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"\n label="${tool.name} on ${on_string}: TAD domains" />\n <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"\n format="gff" label="${tool.name} on ${on_string}: Boundary information plus score" />\n- \n+\n <data name="tad_score" from_work_dir="galaxy_tad_prefix_tad_score.bm"\n format="bedgraph" label="${tool.name} on ${on_string}: TAD information in bm file" />\n \n@@ -108,69 +108,71 @@\n <output name="domains" file="find_TADs/multiFDR_domains.bed" ftype="bed" compare="sim_size" delta="35000" />\n <output name="score" file="find_TADs/multiFDR_score.bedgraph" ftype="bedgraph" compare="sim_size" delta="35000" />\n <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />\n- <output name="matrix_output" file="find_TADs/multiFDR_zscore_matrix.h5" ftype="h5" compare="sim_size" delta="50000" />\n </test>\n </tests>\n <help><![CDATA[\n-Calculate TADs\n-==============\n+Calculate Topologic Associated Domains\n+======================================\n+\n+Toplogical domains (TADs) are large mainly self-interacting domains. Chromatin interactions occur with higher frequency within a TAD as between TADs. More information_.\n \n-Topological associated domains (TADs) are regions on the DNA which tend to interact within the region a lot, but not outside their boundaries. More information_.\n+_________________\n+\n+Usage\n+-----\n \n-Calculation\n-------------\n-``hicFindTADs`` computes the TAD regions in two steps: In a first step it computes a TAD-separation score based on a z-score matrix for all bins. The z-score is defined as:\n+This tool must be used on unmerged matrices (restiction enzyme resolution) produced by ``hicBuildMatrix`` and corrected by ``hicCorrectMatrix``.\n+\n+_________________\n \n-\xe2\x80\x9cThe absolute value of z represents the distance between the raw score and the population mean in \n-units of the standard deviation. z is negative when the raw score is below the mean, positive when above.\xe2\x80\x9d \n-[Source_].\n+Computation detail'..b'he population mean in\n+ units of the standard deviation. z is negative when the raw score is below the mean, positive when above.\xe2\x80\x9d\n+ [Source_].\n \n .. image:: $PATH_TO_IMAGES/z-score.svg\n :width: 100\n- \n+\n `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_\n \n In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.\n \n-\n-Input\n------\n-\n-Parameters\n-__________\n-- contact matrix to compute the TADs on\n-- minimum window length\n-- maximum window length\n-- step size\n-- multiple testing correction\n-- minimum threshold\n-- minimum distance\n-\n-\n-hicFindTADs tries to identify sensible parameters but those can be change to identify more stringent set of boundaries.\n+_________________\n \n Output\n ------\n \n-- Boundary positions as a bed file\n-- Matrix with multi-scale TAD scores as a bedgraph \n-- TAD domains as a bed file\n-- Boundary information plus score as gff\n-- TAD information in bm file\n-- Z-score matrix in h5\n+**hicFindTADs** produces multiple outputs:\n+\n+- TAD boundaries positions as a BED file and TAD separation score.\n+- TAD boundaries positions with delta, p-value and TAD separation score as GFF.\n+- TAD domains as a BED file.\n+- TAD seperation score as bigwig (bw), bedgraph and numpy array (npz) format. These files can be used to plot the so-called TAD insulation score or TAD separation score along the genome or at specific regions. This score is much more reliable across samples than the number of TADs or the TADs width that can vary depending on the sequencing depth because of the lack of information at certain bins, and depending on the parameters used with this tool.\n+- Matrix with multi-scale TAD scores as a bed-matrix (bm) file that can be plotted inside ``hicPlotTADs`` to nicely display TAD insulation score alongside Hi-C heatmap and other datasets.\n+- Z-score matrix in h5 format that is useful to quickly test the --thresholdComparisons, --delta and --correctForMultipleTesting parameters by using the --TAD_sep_score_prefix option pointing to this zscore_matrix.h5 file (will be added in a future update).\n+\n+_________________\n \n-The calulated TAD regions can be plotted with ``hicPlotTADs``.\n+Usage hints\n+-----------\n \n+It is mandatory to test multiple parameters of TAD calling with **hicFindTADs** before making conclusions about the number of TADs in a given sample or before comparing TAD calling between multiple conditions. In order to compare numerous TAD calling parameters at once, it is recommended to use ``hicPlotTADs``, below you can find a plot where multiple TAD calling parameters are displayed for *Drosophila melanogaster* embryos:\n \n-.. image:: $PATH_TO_IMAGES/master_TADs_plot.png\n- :width: 80 %\n+.. image:: $PATH_TO_IMAGES/hicFindTADs_TAD_calling_comparison.png\n+ :width: 65 %\n \n+We can see that the fourth set of **hicFindTADs** parameters with a threshold of 0.001 gives the best results in terms of TAD calling compared to the corrected Hi-C counts distribution and compared to the enrichment of H3K36me3, which is known to be enriched at TAD boundaries in *Drosophila melanogaster*.\n \n+_________________\n \n For more information about HiCExplorer please consider our documentation on readthedocs.io_\n \n .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html\n-.. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score \n+.. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score\n .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_\n ]]></help>\n <expand macro="citations" />\n' |
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| diff -r 43332e51a712 -r b05f292d220c involucro |
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| diff -r 43332e51a712 -r b05f292d220c macros.xml --- a/macros.xml Wed Mar 07 03:46:54 2018 -0500 +++ b/macros.xml Fri Apr 27 03:39:27 2018 -0400 |
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| @@ -1,7 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">2.1</token> - + <token name="@WRAPPER_VERSION@">2.1.2</token> <token name="@USE_RANGE@"> #if $use_range.select_use_range == "yes_use_range": --range $range_min:$range_max @@ -28,7 +27,7 @@ </xml> <xml name="use_range"> <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range --> - <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range"> + <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range" help="If given, only counts within the specified range are considered."> <option value="no_use_range">No restriction</option> <option value="yes_use_range">Only consider counts within a range</option> </param> @@ -40,8 +39,8 @@ </xml> <xml name="range"> - <param name="range_min" type="integer" value="" min="0"/> - <param name="range_max" type="integer" value="" min="0"/> + <param name='range_min' label="Minimum range to consider interactions" type="integer" value="" min="0" help="The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions."/> + <param name='range_max' label="Maximum range to consider interactions" type="integer" value="" min="0"/> </xml> <xml name="colormap"> @@ -189,9 +188,9 @@ <xml name="multiple_input_matrices"> - <repeat name="input_files" title="HiC Matrix files" min="2"> + <repeat name="input_files" title="Hi-C Matrix files" min="2"> <param name="matrix" type="data" format="h5,cool" - label="HiC Matrix file" + label="Hi-C Matrix file" help=""/> <param name="mlabel" type="text" size="30" optional="true" value="" label="Label" |
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| diff -r 43332e51a712 -r b05f292d220c macros.xml.orig --- a/macros.xml.orig Wed Mar 07 03:46:54 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,585 +0,0 @@\n-<macros>\n- <token name="@THREADS@">\\${GALAXY_SLOTS:-4}</token>\n-<<<<<<< HEAD\n- <token name="@WRAPPER_VERSION@">2.0</token>\n-\n- <token name="@USE_RANGE@">\n- #if $use_range.select_use_range == "yes_use_range":\n- --range $range_min:$range_max\n- #end if\n- </token>\n-\n-=======\n- <token name="@WRAPPER_VERSION@">2.1alpha1</token>\n->>>>>>> joachimwolff-master\n- <xml name="requirements">\n- <requirements>\n- <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>\n- <yield />\n- </requirements>\n- <version_command>@BINARY@ --version</version_command>\n- </xml>\n-\n- <xml name="citations">\n- <citations>\n- <citation type="doi">10.5281/zenodo.1133705</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- <xml name="use_range">\n- <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->\n- <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">\n- <option value="no_use_range">No restriction</option>\n- <option value="yes_use_range">Only consider counts within a range</option>\n- </param>\n- <when value="no_use_range"/>\n- <when value="yes_use_range">\n- <param name="range_min" type="integer" value="" min="0"/>\n- <param name="range_max" type="integer" value="" min="0"/>\n- </when>\n- </conditional>\n- </xml>\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: https://matplotlib.org/examples/color/colormaps_reference.html">\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="'..b'/>\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- <xml name="track_input_h5_macro">\n- <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>\n- </xml>\n- <xml name="track_input_bed_macro">\n- <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>\n- </xml>\n- <xml name="track_input_bedgraph_macro">\n- <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format"/>\n- </xml>\n- <xml name="track_input_bigwig_macro">\n- <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_bedgraph_matrix_macro">\n- <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format"/>\n- </xml>\n- <xml name="track_input_tabular_macro">\n- <param name="track_input_tabular" type="data" format="tabular" label="Track file tabular format"/>\n- </xml>\n- <xml name="plot_title">\n- <param name="title" type="text" optional="true" label="Plot title"/>\n- </xml>\n-\n- <xml name="spacer_macro">\n- <param name="spacer_width" type="float" value="" optional="True"\n- label="Include spacer at the end of the track." help="Width of the spacer." />\n- </xml>\n- <xml name="fontsize_macro">\n- <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />\n- </xml>\n-</macros>\n' |
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