\${GALAXY_SLOTS:-4}
3.4.2
#if $use_range.select_use_range == "yes_use_range":
--range $range_min:$range_max
#end if
hicexplorer
@BINARY@ --version
#if $chromosome_list:
#set $chromosomes = []
#for $chrom in $chromosome_list:
#silent $chromosomes.append("'%s'" % $chrom.chromosomes)
#end for
#set $chromosome_string = ' '.join($chromosomes)
--chromosomes $chromosome_string
#end if
10.5281/zenodo.1133705
#set $matrices = []
#set $mlabels = []
#for $counter, $i in enumerate($input_files):
ln -s '$i.matrix' '${counter}_matrix.$i.matrix.ext';
#silent $matrices.append( '\'%s_matrix.%s\'' % ($counter, $i.matrix.ext))
#if str($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)
#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
.. 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://hicexplorer.readthedocs.org
#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
#if $source.ref_source=="history":
--genome $source.input1
#else:
--genome "${source.input1_2bit.fields.path}"
#end if
((
output['showOutputSettings'] == 'yes' and
output['saveMatrix'] is True
))
((
output['showOutputSettings'] == 'yes' and
output['saveData'] is True
))
((
output['showOutputSettings'] == 'yes' and
output['saveSortedRegions'] is True
))