# HG changeset patch
# User iuc
# Date 1524814357 14400
# Node ID ec59bf4c3d06ef27c5c0d2525a834e911806e33f
# Parent ccd1d30138274f0b9e872a02edd8ce505ace1f51
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r ccd1d3013827 -r ec59bf4c3d06 hicAggregateContacts.xml
--- a/hicAggregateContacts.xml Wed Mar 07 03:37:18 2018 -0500
+++ b/hicAggregateContacts.xml Fri Apr 27 03:32:37 2018 -0400
@@ -1,5 +1,6 @@
+
- Takes a list of positions in the hic-matrix and makes a pooled image
+ allow plotting of aggregated Hi-C contacts between regions specified in a file
hicAggregateContacts
macros.xml
@@ -64,21 +65,21 @@
-
+
+ label="Interactions between regions in first and second BED file are plotted"/>
-
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+ help="The bed regions will be centered between -half number of bins
+ and +half number of bins indicated." />
-
+ cases, you might prefer kmeans.">
+
@@ -111,15 +112,18 @@
help="Clustering is by default carried out on the whole
submatrices. If this parameter is given, the
clustering is only carried out based on the submatrix
- diagonal (representing values at the same distance to each other)" />
+ diagonal (representing values at the same distance to each other)." />
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diff -r ccd1d3013827 -r ec59bf4c3d06 involucro
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diff -r ccd1d3013827 -r ec59bf4c3d06 macros.xml
--- a/macros.xml Wed Mar 07 03:37:18 2018 -0500
+++ b/macros.xml Fri Apr 27 03:32:37 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 $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
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-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
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- #if $source.ref_source=="history":
- --genome $source.input1
- #else:
- --genome "${source.input1_2bit.fields.path}"
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diff -r ccd1d3013827 -r ec59bf4c3d06 static/images/hicAggregateContacts.png
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diff -r ccd1d3013827 -r ec59bf4c3d06 static/images/hicCompareMatrices_QC_log2_m50_matrix_plot (1).png
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diff -r ccd1d3013827 -r ec59bf4c3d06 test-data/compare_matrices_log2ratio.h5
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diff -r ccd1d3013827 -r ec59bf4c3d06 test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:37:18 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:32:37 2018 -0400
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