| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.0 |
| bam_to_scidx |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| openjdk | 8.0.112 | package |
| Additional information about this tool |
ln -s '${input_bam}' localbam.bam &&
ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
java -jar '$__tool_directory__/BAMtoscIDX.jar'
-b localbam.bam
-i localbam.bam.bai
-p $require_proper_mate_pairing
-r $read
#if str($min_insert_size):
-m $min_insert_size
#end if
#if str($max_insert_size):
-M $max_insert_size
#end if
-o '$output'
1>/dev/null
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
require_proper_mate_pairing: 1 read: 0 input_bam: input.bam |
output: output.scidx |
input.bam output.scidx |