# HG changeset patch
# User bgruening
# Date 1476048943 14400
# Node ID 4aa65933bc9b4e5da999fe967e279b49b7d39f66
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
diff -r 000000000000 -r 4aa65933bc9b _hicExport._xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/_hicExport._xml Sun Oct 09 17:35:43 2016 -0400
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+ saves a HiC Matrix in text format
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+ hicExport
+ macros.xml
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diff -r 000000000000 -r 4aa65933bc9b hicFindEnrichedContacts.xml
diff -r 000000000000 -r 4aa65933bc9b hicPlotDistVsCounts.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotDistVsCounts.xml Sun Oct 09 17:35:43 2016 -0400
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+ distance vs HiC counts plot per chromosome
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+ hicPlotDistVsCounts
+ macros.xml
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diff -r 000000000000 -r 4aa65933bc9b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Oct 09 17:35:43 2016 -0400
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+ --numberOfProcessors "\${GALAXY_SLOTS:-4}"
+ 1.2
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+ hicexplorer
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+ @BINARY@ --version
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+ 10.5281/zenodo.159780
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+ #set $matrices = []
+ #set $mlabels = []
+ #for $counter, $i in enumerate($input_files):
+ ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
+ #silent $matrices.append( '%s.npz.h5' % $counter )
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+ #if str($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`_.
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+.. _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://github.com/fidelram/deepTools/wiki/
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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['showOutputSettings'] == 'yes' and
+ 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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