| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.30.0.3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.19.0 |
| bedtools_map |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bedtools | 2.30.0 | package |
| Additional information about this tool |
bedtools map
-a '${inputA}'
-b '${inputB}'
$strand
#set $col = list()
#set $op = list()
#for $item in $c_and_o_argument_repeat:
#silent $col.append( str($item.col) )
#silent $op.append( str($item.operation) )
#end for
#if $col:
-c #echo ','.join($col)#
-o #echo ','.join($op)#
#end if
#if str($overlap):
-f $overlap
#end if
#if str($overlapB):
-F $overlapB
#end if
$reciprocal
$split
$header
#if $genome_file_opts.genome
-g
#if $genome_file_opts.genome_file_opts_selector == "loc":
'$genome_file_opts.genome.fields.len_path'
#elif $genome_file_opts.genome_file_opts_selector == "hist":
'$genome_file_opts.genome'
#end if
#end if
> '${output}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputA: mapBed1.bed inputB: mapBed2.bed c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: mean |
name: value |
mapBed1.bed mapBed2.bed value |
| Test-2 |
inputA: mapBed1.bed inputB: mapBed2.bed c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: collapse |
name: value |
mapBed1.bed mapBed2.bed value |
| Test-3 |
inputA: mapBed1.bed inputB: mapBed2.bed strand: -S c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: collapse |
name: value |
mapBed1.bed mapBed2.bed value |
| Test-4 |
inputA: mapBed1.bed inputB: mapBed2.bed strand: -s c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: collapse |
name: value |
mapBed1.bed mapBed2.bed value |
| Test-5 |
inputA: mapBed3.bed inputB: mapBed4.bed strand: -s c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: collapse genome_file_opts|genome: mm9.len genome_file_opts|genome_file_opts_selector: hist |
name: value |
mapBed3.bed mapBed4.bed mm9.len value |
| Test-6 |
inputA: mapBed3.bed inputB: mapBed4.bed strand: -s c_and_o_argument_repeat_0|col: 5 c_and_o_argument_repeat_0|operation: collapse genome_file_opts|genome: mm9 genome_file_opts|genome_file_opts_selector: loc |
name: value |
mapBed3.bed mapBed4.bed value |