--numberOfProcessors "\${GALAXY_SLOTS:-4}"2.5.0pythondeeptools@BINARY@ --version
#if $advancedOpt.doExtendCustom.doExtend == 'custom':
--extendReads $advancedOpt.doExtendCustom.extendReadsValue
#else if $advancedOpt.doExtendCustom.doExtend == 'yes':
--extendReads
#end if
$advancedOpt.ignoreDuplicates
$advancedOpt.centerReads
#if $advancedOpt.minMappingQuality:
--minMappingQuality '$advancedOpt.minMappingQuality'
#end if
#if $advancedOpt.samFlagInclude:
--samFlagInclude $advancedOpt.samFlagInclude
#end if
#if $advancedOpt.samFlagExclude:
--samFlagExclude $advancedOpt.samFlagExclude
#end if
#if $advancedOpt.minFragmentLength:
--minFragmentLength $advancedOpt.minFragmentLength
#end if
#if $advancedOpt.maxFragmentLength:
--maxFragmentLength $advancedOpt.maxFragmentLength
#end if
$advancedOpt.metagene
#if $advancedOpt.transcriptID:
--transcriptID $advancedOpt.transcriptID
#end if
#if $advancedOpt.exonID:
--exonID $advancedOpt.exonID
#end if
#if $advancedOpt.transcript_id_designator:
--transcript_id_designator $advancedOpt.transcript_id_designator
#end if
#if str($plotting_type.zMin) != "":
--zMin $plotting_type.zMin
#end if
#if str($plotting_type.zMax) != "":
--zMax $plotting_type.zMax
#end if
--colorMap '$plotting_type.colorMap'
$plotting_type.plotNumbers
--plotTitle '$plotting_type.plotTitle'
#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
#if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
#if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
--hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
#end if
#end if
#end if
.. class:: infomark
For more information on the tools, please visit our `help site`_.
If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://deeptools.readthedocs.org/
10.1093/nar/gkw257
0:
--BED #echo ' '.join($files)#
--regionLabels #echo ' '.join($labels)#
#end if
]]>
#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['saveSortedRegions'] is True
))