# HG changeset patch
# User bgruening
# Date 1476048972 14400
# Node ID 83b1998b0ec624567df5dd246be95e9914e074fd
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
diff -r 000000000000 -r 83b1998b0ec6 _hicExport._xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/_hicExport._xml Sun Oct 09 17:36:12 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 83b1998b0ec6 hicFindEnrichedContacts.xml
diff -r 000000000000 -r 83b1998b0ec6 hicPlotTADs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotTADs.xml Sun Oct 09 17:36:12 2016 -0400
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+ Plots the diagonal, and some values close to the diagonal of a HiC matrix
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+ hicPlotTADs
+ macros.xml
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+## lines that start with '#' are comment lines
+## and are not interpreted by the program
+## the different tracks are represented by sections in this file
+## each section starts with a header of the form [hic]
+## the content of the section label (in the previous example 'hic') is irrelevant for
+## plotting and only used to tell the user when something goes wrong.
+## There are two exceptions for this, the [x-axis] and the [spacer] sections
+## that use the secion label to determine the action.
+
+
+#for $counter, $track in enumerate($tracks):
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+[hic_section_$counter]
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+file = $track.track_input
+title = $track.title
+colormap = $track.colorMap
+depth = 100000
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+##color = black
+##width = 1.5
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+## auto is possible
+#if not $track.min_value:
+min_value = auto
+#else:
+min_value = $track.min_value
+#end if
+#if not $track.max_value:
+max_value = auto
+#else:
+max_value = $track.max_value
+#end if
+transform = $track.transform
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+##boundaries_file = conductance_vs_hic/boundaries_all.bed
+x labels = yes
+type = arcplot
+type = interaction
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+##file_type = h5
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+#if $track.track_input.ext == "bedgraph":
+file_type = bedgraph_matrix
+#else:
+file_type = $track.track_input.ext
+#end if
+
+## show masked bins plots as white lines
+## those bins that were not used during the correction
+## the default is to extend neighboring bins to
+## obtain an aesthetically pleasant output
+show_masked_bins = $track.show_masked_bins
+
+
+## to turn off/on printing of labels
+labels = $track.plot_lables
+## options are 'genes' or 'domains'.
+type = $track.type_of_data
+## optional: font size can be given if default are not good
+fontsize = $track.fontsize
+
+#if $track.orientation
+orientation = $track.orientation
+#end if
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+#if $track.plotting_type
+type = lines
+#end if
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+#end for
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+[x-axis]
+# optional
+fontsize=20
+# optional, options are top or bottom
+where=top
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+# to insert a space simple add a
+# section title [spacer]
+[spacer]
+#optional
+width = 0.1
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diff -r 000000000000 -r 83b1998b0ec6 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Oct 09 17:36:12 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' % $counter )
+
+ #if str($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://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)
+
+ ##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)
+
+ ##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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