| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.6 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.5 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.4 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.3 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/0.0.2 |
| toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/0.0.1 |
| samtools_slice_bam |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| samtools | 1.22 | package |
| Additional information about this tool |
ln -s '${input_bam}' temp_input.bam &&
ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai &&
#if str($slice_method.slice_method_selector) == "bed":
samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
#elif str($slice_method.slice_method_selector) == "chr":
samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
#elif str($slice_method.slice_method_selector) == "man":
samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
#for $region in $slice_method.regions:
"${region.chrom}:${region.start}-${region.end}"
#end for
&&
#end if
samtools sort
-O bam
-T "\${TMPDIR:-.}"
-@ \${GALAXY_SLOTS:-1}
-o '${output_bam}'
unsorted_output.bam
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_bam: bam-slice-input.bam slice_method|input_interval: bam-slice.bed slice_method|slice_method_selector: bed |
name: value |
bam-slice-input.bam bam-slice.bed value |
| Test-2 |
input_bam: bam-slice-input.bam slice_method|refs: chrM slice_method|slice_method_selector: chr |
name: value |
bam-slice-input.bam value |
| Test-3 |
input_bam: bam-slice-input.bam slice_method|regions_0|chrom: chrM slice_method|regions_0|start: 1 slice_method|regions_0|end: 1000 slice_method|slice_method_selector: man |
name: value |
bam-slice-input.bam value |