| Previous changeset 8:f7d344dacfeb (2018-03-07) Next changeset 10:bfa1c014f64a (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:
hicCorrectMatrix.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 f7d344dacfeb -r ac80bd0a96ca hicCorrectMatrix.xml --- a/hicCorrectMatrix.xml Wed Mar 07 03:24:24 2018 -0500 +++ b/hicCorrectMatrix.xml Fri Apr 27 03:29:59 2018 -0400 |
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| b'@@ -1,5 +1,5 @@\n <tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n- <description>Runs Dekker\'s iterative correction over a hic matrix.</description>\n+ <description>run Imakaev\'s iterative correction over a Hi-C contact matrix.</description>\n <macros>\n <token name="@BINARY@">hicCorrectMatrix</token>\n <import>macros.xml</import>\n@@ -64,7 +64,7 @@\n <inputs>\n <expand macro=\'matrix_h5_cooler_macro\' />\n <conditional name="mode">\n- <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">\n+ <param name="mode_selector" type="select" label="Mode">\n <option value="diagnostic_plot">Diagnostic plot</option>\n <option value="correct">Correct matrix</option>\n </param>\n@@ -105,7 +105,7 @@\n <repeat name="chromosomes" min="0"\n title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.\n The order of the given chromosomes will be kept for the resulting corrected matrix">\n- <param name="chromosome" type="text" value="" >\n+ <param name="chromosome" type="text" value="" label=\'chromosome (one per field)\'>\n <validator type="empty_field" />\n </param>\n </repeat>\n@@ -117,10 +117,10 @@\n <when input="mode.outputFormat" value="cool" format="cool" />\n </change_format>\n <filter>mode[\'mode_selector\'] == "correct"</filter>\n- \n+\n </data>\n- \n- \n+\n+\n <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">\n <filter>mode[\'mode_selector\'] == "diagnostic_plot"</filter>\n </data>\n@@ -128,16 +128,17 @@\n <tests>\n <test>\n <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>\n- \n+\n <param name="mode_selector" value="correct"/>\n <repeat name="chromosomes">\n <param name="chromosome" value="chrUextra"/>\n </repeat>\n <repeat name="chromosomes">\n <param name="chromosome" value="chr3LHet"/>\n- </repeat> \n+ </repeat>\n <param name=\'outputFormat\' value=\'h5\'/>\n-\n+ <param name=\'filterThreshold_low\' value=\'-2.0\' />\n+ <param name=\'filterThreshold_large\' value=\'4\' />\n <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>\n </test>\n <test>\n@@ -148,79 +149,82 @@\n </repeat>\n <repeat name="chromosomes">\n <param name="chromosome" value="chr3LHet"/>\n- </repeat> \n+ </repeat>\n <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>\n </test>\n </tests>\n <help><![CDATA[\n \n-Matrix correction\n-==================\n+Hi-C contact matrix correction\n+==============================\n \n-``hicCorrectMatrix`` runs Dekker\'s iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix, \n-it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only \n-chromosomes, as scaffolds create problems with matrix correction. Therefore \n-we use the chromosome names (1-19, X, Y) here. \n- \n+**hicCorrectMatrix** runs Imakaev\'s iterative correction, described in `Imakaev et al. (2012)`_, over a Hi-C matrix. For the matrix correction to be efficient,\n+it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only full length\n+chromosomes, as scaffolds create problems with matrix correction. Therefore we use the chromosome names (1-19, X, Y) here.\n+\n **Important**: Use \xe2\x80\x98chr1 chr2 chr3 etc.\xe2\x80\x99 if your genome index uses chromosome names with the \xe2\x80\x98chr\xe2\x80\x99 prefix.\n \n-Matrix correction works in tw'..b'py number variations.\n+\n+To aid in the identification of bins with low and high read coverage, the ``diagnostic plot`` function of **hicCorrectMatrix** must be used.\n+\n+Indeed, **hicCorrectMatrix** works in two steps:\n \n-Input\n+ - **Diagnostic plot**: 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.\n+\n+ - **Correct**: The second step removes the bins outside of the defined thresholds and perfroms the iterative correction.\n+\n+_________________\n+\n+Usage\n -----\n \n-\n-Diagnostic plot\n-~~~~~~~~~~~~~~~~\n-Plots a histogram of the coverage per bin together with the\n-modified z-score based on the median absolute deviation\n-method.\n-\n-See Boris Iglewicz and David Hoaglin 1993, Volume 16: \n-How to Detect and Handle Outliers The ASQC Basic References in Quality Control: Statistical Techniques,\n-Edward F. Mykytka, Ph.D., Editor.\n-\n-Parameters\n-__________\n-- the contact matrix\n-- Max value for the x-axis in counts per bin\n-- include chromosomes\n+This tool must be used on uncorrected matrices at restriction enzyme resolution or with merged bins (``hicMergeMatrixBins``).\n \n-\n-Correct\n-~~~~~~~\n-\n-Run the iterative correction. \n-\n-Parameters\n-__________\n-- number of iterations\n-- inflation cutoff\n-- trans region cutoff\n-- sequenced count cutoff\n-- skip diagonal counts\n-- normalize each chromosome separately\n-- remove bins of low coverage\n-- remove bins of large coverage\n-- include chromosomes\n+_________________\n \n Output\n ------\n \n- Diagnostic plot:\n+Diagnostic plot\n+_______________\n+\n+The diagnostic plot consists of a bar plot of the contacts coverage per bins size together with the\n+modified z-score based on the Median Absolute Deviation (MAD) method.\n+\n+See Boris Iglewicz and David Hoaglin 1993, Volume 16:\n+How to Detect and Handle Outliers The ASQC Basic References in Quality Control: Statistical Techniques,\n+Edward F. Mykytka, Ph.D., Editor.\n+\n+Using this diagnostic plot, a user can decide if values\n+with a too low (and/or too high) number of contacts in respect to their genomic distance should\n+be removed from the data before the correction applies.\n \n- .. image:: $PATH_TO_IMAGES/diagnostic_plot.png\n- :width: 70%\n- \n- Correct:\n- - the corrected contact matrix\n+Moreover, the shown distribution should be a Gaussian bell. If it doesn\xe2\x80\x99t follow a Gaussian distribution\n+this is an indicator that the used data is of bad quality or that the used contact matrix\n+is maybe not the one that should be used. It can happen that users select for example a merge\n+matrix with a lower resolution that was previously needed for plotting. In such cases the\n+diagnostic plot helps to detect this and prevent the user from running the analysis on a wrong dataset.\n+\n+\n+.. image:: $PATH_TO_IMAGES/diagnostic_plot.png\n+ :width: 50%\n+\n+On the example plot above, a user can then use the lower threshold defined by the MAD method (black bold bar), or define its own threshold based on the contacts distribution.\n+\n+Correct\n+_______\n+\n+Run the iterative correction and outputs the corrected matrix. This matrix can then be used with all downstream analysis tools such as ``hicPlotMatrix``, ``hicPlotTADs``, ``hicPlotViewpoint``, ``hicAggregateContacts`` for **visualization of Hi-C data**, ``hicCorrelate``, ``hicPlotDistVsCounts``, ``hicTransform``, ``hicFindTADs``, ``hicPCA`` **for data and scores computation on Hi-C data**.\n+\n+It is noteworthy that ``hicSumMatrices`` and ``hicMergeMatrixBins`` **must be performed on uncorrected matrices**.\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-\n-.. _`Imakaev 2012`: http://doi.org/doi:10.1038/nmeth.2148\n+.. _`Imakaev et al. (2012)`: http://doi.org/doi:10.1038/nmeth.2148\n ]]></help>\n <expand macro="citations" />\n </tool>\n-\n' |
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| diff -r f7d344dacfeb -r ac80bd0a96ca involucro |
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| diff -r f7d344dacfeb -r ac80bd0a96ca macros.xml --- a/macros.xml Wed Mar 07 03:24:24 2018 -0500 +++ b/macros.xml Fri Apr 27 03:29:59 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 f7d344dacfeb -r ac80bd0a96ca macros.xml.orig --- a/macros.xml.orig Wed Mar 07 03:24:24 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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