| Previous changeset 8:707f691c974c (2018-03-07) Next changeset 10:c6ff5b14d49e (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:
hicBuildMatrix.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 707f691c974c -r 495ae38f6e0d hicBuildMatrix.xml --- a/hicBuildMatrix.xml Wed Mar 07 03:42:32 2018 -0500 +++ b/hicBuildMatrix.xml Fri Apr 27 03:35:56 2018 -0400 |
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| b'@@ -1,5 +1,5 @@\n <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">\n- <description>creates a contact matrix</description>\n+ <description>create a contact matrix</description>\n <macros>\n <token name="@BINARY@">hicBuildMatrix</token>\n <import>macros.xml</import>\n@@ -38,8 +38,10 @@\n #end if\n \n --outFileName matrix.$outputFormat\n- \n- --outBam ./unsorted.bam\n+\n+ #if $outBam_Boolean:\n+ $outBam_Boolean ./unsorted.bam\n+ #end if\n \n $keepSelfCircles\n \n@@ -52,7 +54,7 @@\n #end if\n \n --threads @THREADS@\n- \n+\n --QCfolder ./QCfolder\n &&\n mv ./QCfolder/* $qc.files_path/\n@@ -60,13 +62,16 @@\n mv $qc.files_path/hicQC.html $qc\n && mv $qc.files_path/*.log raw_qc\n && mv matrix.$outputFormat matrix\n- && samtools sort ./unsorted.bam -o sorted.bam\n- \n+ #if $outBam_Boolean:\n+ && samtools sort ./unsorted.bam -o sorted.bam\n+ #end if\n+\n ]]>\n </command>\n <inputs>\n- <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">\n- <param name="samFile" type="data" format="sam,bam"/>\n+ <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" \n+ help="Please use the special BAM datatype: qname_input_sorted.bam and use for \'bowtie2\' the \'--reorder\' option to create a BAM file.">\n+ <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>\n </repeat>\n <conditional name="restrictionCutFileBinSize_conditional">\n <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">\n@@ -106,28 +111,42 @@\n \n <expand macro="minMappingQuality" />\n \n- <param argument="--danglingSequence" type="text" optional="true" label="The dangling sequence"\n- help="Dangling end sequence left by the restriction enzyme. For DpnII for example, \n- the dangling end is the same restriction sequence. This is used\n- to discard reads that end/start with such sequence \n- and that are considered un-ligated fragments or \n- \'dangling-ends\'. If not given, such statistics will \n- not be available."/>\n+ <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"\n+ help="Sequence left by the restriction enzyme after cutting.\n+ Each restriction enzyme recognizes a different DNA sequence and, \n+ after cutting, they leave behind a specific \xe2\x80\x98sticky\xe2\x80\x99 end or dangling end sequence.\n+ For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT. \n+ For DpnII, the restriction site and dangling end sequence are the same: GATC. \n+ This information is easily found on the description of the restriction enzyme.\n+ The dangling sequence is used to classify and report reads whose 5\xe2\x80\x99 end starts with such sequence as dangling-end reads.\n+ A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>\n+\n+ <param name=\'outBam_Boolean\' type=\'boolean\' truevalue=\'--outBam\' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file"\n+ help="A bam\n+ file containing all valid Hi-C reads can be created\n+ using this option. This bam file could be useful to\n+ inspect the distribution of valid Hi-C reads pairs or\n+ for other downstream analyses, but is not used by any\n+ HiCExplorer tool. Computation will be significantly\n+ '..b' left pairs\n-- right pairs \n+A quality report is produced alongside the contact matrix.\n \n .. image:: $PATH_TO_IMAGES/hicQC.png\n- :width: 70 %\n+ :width: 40%\n+\n+Several plots, that are described in details below, are comprised inside this report.\n+\n+.. image:: $PATH_TO_IMAGES/hicQC_pairs_sequenced.png\n+ :width: 40%\n+\n+On the plot above, we can see how many reads were sequenced per sample (pairs considered), how many reads were mappable, unique and of high quality and how many reads passed all quality controls and are thus useful for further analysis (pairs used). All quality controls used for read filtering are explained below.\n+\n+.. image:: $PATH_TO_IMAGES/hicQC_unmappable_and_non_unique.png\n+ :width: 40%\n+\n+The figure above contains the fraction of reads with respect to the total number of reads that did not map, that have a low quality score or that didn\'t map uniquely to the genome. In our example we can see that Sample 3 has the highest fraction of pairs used. We explain the differences between the three samples on the plot below.\n+\n+.. image:: $PATH_TO_IMAGES/hicQC_pairs_discarded.png\n+ :width: 40%\n+\n+This figure contains the fraction of read pairs (with respect to mappable and unique reads) that were discarded when building the Hi-C matrix. You can find the description of each category below:\n+\n+ - **Dangling ends:** reads that start with the restriction site and constitute reads that were digested but not ligated. Sample 1 in our example has a high fraction of dangling ends (and thus a low proportion of pairs used). Reasons for this can be inefficient ligation or insufficient removal of danging ends during samples preparation.\n \n+ - **Duplicated pairs:** reads that have the same sequence due to PCR amplification. For example, Sample 2 was amplified too much and thus has a very high fraction of duplicated pairs.\n+\n+ - **Same fragment:** read mates facing inward, separated by up to 800bp that do not have a restriction enzyme site in between. These read pairs are not valid Hi-C pairs and are thus discarded from further analyses.\n+\n+ - **Self circle:** read pairs within 25kb with \'outward\' read orientation.\n+\n+ - **Self ligation:** read pairs with a restriction site in between that are within 800bp.\n+\n+.. image:: $PATH_TO_IMAGES/hicQC_distance.png\n+ :width: 40%\n+\n+The figure above contains the fraction of read pairs (with respect to mappable reads) that compose inter chromosomal, short range (< 20kb) or long range contacts. Inter chromosomal reads of a wild-type sample are expected to be low. Trans-chromosomal contacts can be primarily considered as random ligation events. These would be expected to contribute to technical noise that may obscure some of the finer features in the Hi-C datasets (Nagano *et al.* 2015, Comparison of Hi-C results using in-solution versus in-nucleus ligation, doi: https://doi.org/10.1186/s13059-015-0753-7). As such, a high fraction of inter chromosomal reads is an indicator of low sample quality, but it can also be associated to cell cycle changes (Nagano *et al.* 2018, Cell-cycle dynamics of chromosomal organisation at single-cell resolution, doi: https://doi.org/10.1038/nature23001).\n+\n+Short range and long range contacts proportions can be associated to how the fixation is performed during Hi-C sample preparation. These two proportions also directly impact the Hi-C corrected counts versus genomic distance plots generated by hicPlotDistVsCounts.\n+\n+.. image:: $PATH_TO_IMAGES/hicQC_read_orientation.png\n+ :width: 40%\n+\n+The last figure shows the fractions of inward, outward, left or right read pairs (with respect to mappable reads). Deviations from an equal distribution indicates problems during sample preparation.\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-\n ]]></help>\n <expand macro="citations" />\n </tool>\n' |
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| diff -r 707f691c974c -r 495ae38f6e0d involucro |
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| diff -r 707f691c974c -r 495ae38f6e0d macros.xml --- a/macros.xml Wed Mar 07 03:42:32 2018 -0500 +++ b/macros.xml Fri Apr 27 03:35:56 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 707f691c974c -r 495ae38f6e0d macros.xml.orig --- a/macros.xml.orig Wed Mar 07 03:42:32 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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