| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergedomains/hicexplorer_hicmergedomains/3.6+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergedomains/hicexplorer_hicmergedomains/3.6+galaxy0 |
| hicexplorer_hicmergedomains |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hicexplorer | 3.6 | package |
| Additional information about this tool |
#for $counter, $tadfile in enumerate($domainFiles):
ln -s '$tadfile' '${counter}_tad_file.bed' &&
#end for
#set $m = ' '.join([ '\'%s_tad_file.bed\'' % $counter for $counter, $inputfile in enumerate($domainFiles) ])
hicMergeDomains
--domainFiles $m
#if $proteinFile:
--proteinFile '$proteinFile'
#end if
#if $minimumNumberOfPeaks:
--minimumNumberOfPeaks $minimumNumberOfPeaks
#end if
#if $valueX:
--value $valueX
#end if
#if $percent:
--percent $percent
#end if
--outputMergedList mergedDomains.bed
--outputRelationList relationList.txt
--outputTreePlotFormat pdf
--outputTreePlotPrefix relationship_tree
&& mkdir relationship_plots
&& cp relationship_tree_*.pdf relationship_plots
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
domainFiles: ['hicMergeDomains/10kbtad_domains.bed', 'hicMergeDomains/50kbtad_domains.bed', 'hicMergeDomains/100kbtad_domains.bed'] proteinFile: hicMergeDomains/ctcf_sorted.bed minimumNumberOfPeaks: 2 valueX: 5000 percent: 0.7 |
name: value name: value |
hicMergeDomains/10kbtad_domains.bed hicMergeDomains/50kbtad_domains.bed hicMergeDomains/100kbtad_domains.bed hicMergeDomains/ctcf_sorted.bed value |