# HG changeset patch
# User bgruening
# Date 1490855447 14400
# Node ID 9767c021cd5898c9936b91028ff5ec90bc9a195d
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
diff -r 000000000000 -r 9767c021cd58 _hicExport._xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/_hicExport._xml Thu Mar 30 02:30:47 2017 -0400
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+
+ saves a HiC Matrix in text format
+
+ hicExport
+ macros.xml
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diff -r 000000000000 -r 9767c021cd58 hicBuildMatrix.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/hicBuildMatrix.xml Thu Mar 30 02:30:47 2017 -0400
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+
+ creates a matrix of interactions
+
+ hicBuildMatrix
+ macros.xml
+
+
+ samtools
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diff -r 000000000000 -r 9767c021cd58 hicFindEnrichedContacts.xml
diff -r 000000000000 -r 9767c021cd58 involucro
Binary file involucro has changed
diff -r 000000000000 -r 9767c021cd58 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Mar 30 02:30:47 2017 -0400
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+ --numberOfProcessors "\${GALAXY_SLOTS:-4}"
+ 1.7.1
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+ python
+ 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
+
+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
+
+
+
+ #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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diff -r 000000000000 -r 9767c021cd58 test-data/Li_et_al_2015.h5
Binary file test-data/Li_et_al_2015.h5 has changed
diff -r 000000000000 -r 9767c021cd58 test-data/diagnostic_plot.png
Binary file test-data/diagnostic_plot.png has changed
diff -r 000000000000 -r 9767c021cd58 test-data/dm3_genes.bed.gz
Binary file test-data/dm3_genes.bed.gz has changed
diff -r 000000000000 -r 9767c021cd58 test-data/dm3_genes.bed6.gz
Binary file test-data/dm3_genes.bed6.gz has changed
diff -r 000000000000 -r 9767c021cd58 test-data/domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/domains.bed Thu Mar 30 02:30:47 2017 -0400
@@ -0,0 +1,498 @@
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 9767c021cd58 test-data/hicFindTADs_find_boundaries.bed
diff -r 000000000000 -r 9767c021cd58 test-data/hicFindTADs_find_boundaries.gff
diff -r 000000000000 -r 9767c021cd58 test-data/hicFindTADs_find_domains.bed
diff -r 000000000000 -r 9767c021cd58 test-data/hicFindTADs_find_score.bedgraph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 9767c021cd58 test-data/hicPlotMatrix_result1.svg
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diff -r 000000000000 -r 9767c021cd58 test-data/hicPlotTADs_result1.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 9767c021cd58 test-data/small_test_R1_unsorted.bam
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diff -r 000000000000 -r 9767c021cd58 test-data/small_test_R2_unsorted.bam
Binary file test-data/small_test_R2_unsorted.bam has changed
diff -r 000000000000 -r 9767c021cd58 test-data/small_test_matrix_50kb_res.h5
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diff -r 000000000000 -r 9767c021cd58 test-data/tadScoreFile.tabular_zscore_matrix.h5
Binary file test-data/tadScoreFile.tabular_zscore_matrix.h5 has changed
diff -r 000000000000 -r 9767c021cd58 test-data/tad_classification.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 9767c021cd58 test-data/tad_score.gz
Binary file test-data/tad_score.gz has changed