# HG changeset patch
# User iuc
# Date 1524814607 14400
# Node ID 653c6fead9f9d211994b3cab6b5b5b49c825d36c
# Parent d398f5373c70202e52d93abe3df435d4cd012eec
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r d398f5373c70 -r 653c6fead9f9 hicPlotMatrix.xml
--- a/hicPlotMatrix.xml Wed Mar 07 03:44:12 2018 -0500
+++ b/hicPlotMatrix.xml Fri Apr 27 03:36:47 2018 -0400
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- Plots a HiC matrix heatmap
+ plot a Hi-C contact matrix heatmap
hicPlotMatrix
macros.xml
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#elif str($pca_conditional.pca_type) == '':
#set $pca = ''
#end if
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@BINARY@
--matrix '$matrix_h5_cooler'
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help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless --region2 is given"/>
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Contact matrix plot
=======================
-``hicPlotMatrix`` is a visualization tool for a contact matrix. It supports to plot the whole contact matrix, one or more chromosomes, a region or two regions against each other.
- Additional it can plot the result of a principal component analysis to have a better understanding of A / B compartments.
+**hicPlotMatrix** is a visualization tool for Hi-C contact matrices. It supports to plot genome-wide contact matrices, one or multiple chromosomes, a region or two regions against each other.
+Additionally it can plot the result of a principal component analysis obtained by ``hicPCA`` to have a better understanding of A / B compartments.
-Input
+_________________
+
+Usage
-----
-Parameters
-__________
-- the contact matrix: h5 or cool file format.
-- A title for the plot
-- Score name
-- per chromosome
-- The chromosomes to include in the plot.
-- What to show:
-- The region(s) to plot. This parameter overrides 'chromosome'. If either 'chromosomes' or 'region' is given the full contact matrix is used.
-- log / log1p of the values: It is recommended to use log1p.
-- Colormaps_ for the heatmap.
-- vMin / vMax
-- principal component: a bigwig file containing eigenvector information
+This tool can be used on any h5 or cool Hi-C contact matrix. It is noteworthy that for comparisons of 2 matrices or more, they must all have the same or similar number of contacts.
+
+_________________
Output
------
-The contact matrix plotted for chromosome 1.
+**hicPlotMatrix** outputs a heatmap of a contact matrix in either png or svg format, below is an example of such a plot:
-.. image:: SRR027956.svg
- :width: 60%
+.. image:: $PATH_TO_IMAGES/hicPlotMatrix.png
+ :width: 50%
+Contact matrix of *Drosophila melanogaster* embryos visualized using **hicPlotMatrix**. Hi-C matrix bins were merged to a 25 kb bin size using ``hicMergeMatrixBins`` and the matrix has then been corrected using ``hicCorrectMatrix`` before plotting.
-The contact matrix used with ``--perChr`` and the first eigenvector from the tool ``hicPCA``. For this plot a pearson correlated matrix was used which is computed by creating first an observed / expected matrix and second a pearson correlation matrix. These matricies can be computed with ``hicChangeMatrixType``. The used Hi-C data were published by `Lieberman-Aiden `_ in 2009, `GSE18199 `_.
+Another example is available below using Hi-C data published by `Lieberman-Aiden `_ in 2009, (`GSE18199 `_). A Hi-C contact matrix has been plotted with the ``--perChr`` option and the first eigenvector (pca1) computed by ``hicPCA``. For this plot a pearson correlated matrix was used, which is computed by first creating an observed / expected matrix and then a pearson correlation matrix with ``hicTransform``.
.. image:: $PATH_TO_IMAGES/SRR0279XX_perChr_eigenvector1.png
:width: 70 %
+_________________
+
| For more information about HiCExplorer please consider our documentation on readthedocs.io_
.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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]]>
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diff -r d398f5373c70 -r 653c6fead9f9 involucro
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diff -r d398f5373c70 -r 653c6fead9f9 macros.xml
--- a/macros.xml Wed Mar 07 03:44:12 2018 -0500
+++ b/macros.xml Fri Apr 27 03:36:47 2018 -0400
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\${GALAXY_SLOTS:-4}
- 2.1
-
+ 2.1.2
#if $use_range.select_use_range == "yes_use_range":
--range $range_min:$range_max
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- \${GALAXY_SLOTS:-4}
-<<<<<<< HEAD
- 2.0
-
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- #if $use_range.select_use_range == "yes_use_range":
- --range $range_min:$range_max
- #end if
-
-
-=======
- 2.1alpha1
->>>>>>> joachimwolff-master
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- hicexplorer
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- @BINARY@ --version
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- 10.5281/zenodo.1133705
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- #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)
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- #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
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-.. class:: infomark
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-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
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- #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)
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- ##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
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- #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)]
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- #if $source.ref_source=="history":
- --genome $source.input1
- #else:
- --genome "${source.input1_2bit.fields.path}"
- #end if
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- output['showOutputSettings'] == 'yes' and
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diff -r d398f5373c70 -r 653c6fead9f9 test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:44:12 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:36:47 2018 -0400
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