| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.19.0 |
| bedtools_bamtobed |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bedtools | 2.30.0 | package |
| samtools | 1.9 | package |
| Additional information about this tool |
#if $input.extension in ['bam', 'unsorted.bam', 'qname_input_sorted.bam'] and $option == "-bedpe":
samtools sort -n -@ "\${GALAXY_SLOTS:-4}" -T "\${TMPDIR:-.}" '${input}' > ./input.bam &&
#else
ln -s '${input}' ./input.bam &&
#end if
bedtools bamtobed
$option
$ed_score
$split
#if $tag and str($tag).strip():
-tag '${tag}'
#end if
-i ./input.bam
> '${output}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: srma_in3.bam option: tag: |
name: value |
srma_in3.bam value |
| Test-2 |
input: srma_in3.bam option: tag: NM |
name: value |
srma_in3.bam value |
| Test-3 |
input: bedpeToBam_result1.bam option: -bedpe tag: |
name: value |
bedpeToBam_result1.bam value |