# HG changeset patch
# User iuc
# Date 1524814239 14400
# Node ID 62803bb478808ba1c72a84ee799073996cd1877e
# Parent ea39c587161f7b94cb349497a87b562202172811
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r ea39c587161f -r 62803bb47880 hicPlotDistVsCounts.xml
--- a/hicPlotDistVsCounts.xml Wed Mar 07 03:25:15 2018 -0500
+++ b/hicPlotDistVsCounts.xml Fri Apr 27 03:30:39 2018 -0400
@@ -1,5 +1,5 @@
- distance vs HiC counts plot per chromosome
+ compute distance vs Hi-C counts plot per chromosome
hicPlotDistVsCounts
macros.xml
@@ -33,25 +33,25 @@
]]>
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+
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+ help="If more than one Hi-C matrix is given for each chromosome a new plot is made. Otherewise, a single plot with one line per chromosome is created." />
+ help="Width and height of the plot (in inches). Default is 6 * number of cols, 4 * number of rows. The maximum number of rows is 4. Example: 6 5." />
+ help="This is useful for example to exclude the Y chromosome or to reduce the analysis to only a few chromosomes.">
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diff -r ea39c587161f -r 62803bb47880 involucro
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diff -r ea39c587161f -r 62803bb47880 macros.xml
--- a/macros.xml Wed Mar 07 03:25:15 2018 -0500
+++ b/macros.xml Fri Apr 27 03:30:39 2018 -0400
@@ -1,7 +1,6 @@
\${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 $matrices = []
- #set $mlabels = []
- #for $counter, $i in enumerate($input_files):
- ln -s $i.matrix #echo str($counter)+'_matrix'#;
- #silent $matrices.append( '%s_matrix' % $counter )
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- #if str($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`_.
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-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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- #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 $temp_input_handle.close()
- #silent os.system("ln -s %s %s.bam" % (str($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
- #end for
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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)
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- ##set $files += [str($i.bigwigfile)]
- #if str($i.label.value) != "":
- #set $labels += ["\"%s\"" % ($i.label.value)]
- #else
- #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
- #end if
- #end for
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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['saveMatrix'] is True
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- output['showOutputSettings'] == 'yes' and
- output['saveData'] is True
- ))
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- output['showOutputSettings'] == 'yes' and
- output['saveSortedRegions'] is True
- ))
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diff -r ea39c587161f -r 62803bb47880 static/images/hicAggregateContacts.png
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diff -r ea39c587161f -r 62803bb47880 static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png
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diff -r ea39c587161f -r 62803bb47880 static/images/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot (1).png
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diff -r ea39c587161f -r 62803bb47880 static/images/pulication_plots_viewpoint.png
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diff -r ea39c587161f -r 62803bb47880 test-data/compare_matrices_log2ratio.h5
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diff -r ea39c587161f -r 62803bb47880 test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:25:15 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:30:39 2018 -0400
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