| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/sniffles/sniffles/1.0.12+galaxy0 (this tool) |
| sniffles |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| sniffles | 1.0.12 | package |
| Additional information about this tool |
ln -f -s '${input}' input.bam &&
ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
sniffles
-t \${GALAXY_SLOTS:-2}
-m 'input.bam'
-v '$output'
## general_options
#if $general_options.min_support:
--min_support $general_options.min_support
#end if
--max_num_splits $general_options.max_num_splits
#if $general_options.max_distance:
--max_distance $general_options.max_distance
#end if
#if $general_options.min_length:
--min_length $general_options.min_length
#end if
--minmapping_qual $general_options.minmapping_qual
--num_reads_report $general_options.num_reads_report
#if $general_options.min_seq_size:
--min_seq_size $general_options.min_seq_size
#end if
--min_zmw $general_options.min_zmw
$general_options.cs_string
## clustering_options
$clustering_options.cluster
#if $clustering_options.cluster_support:
--cluster_support $clustering_options.cluster_support
#end if
--allelefreq $clustering_options.allelefreq
--min_homo_af $clustering_options.min_homo_af
--min_het_af $clustering_options.min_het_af
##advanced_options
$advanced_options.report_BND
$advanced_options.not_report_seq
$advanced_options.ignore_sd
$advanced_options.ccs_reads
## parameter_estimation_options
$parameter_estimation_options.skip_parameter_estimation
--del_ratio $parameter_estimation_options.del_ratio
--ins_ratio $parameter_estimation_options.ins_ratio
--max_diff_per_window $parameter_estimation_options.max_diff_per_window
--max_dist_aln_events $parameter_estimation_options.max_dist_aln_events
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: reads_region.bam |
name: value |
reads_region.bam value |
| Test-2 |
input: reads_region.bam general_options|num_reads_report: -1 |
name: value |
reads_region.bam value |
| Test-3 |
input: reads_region.bam general_options|cs_string: True |
name: value |
reads_region.bam value |
| Test-4 |
input: reads_region.bam clustering_options|cluster: True |
name: value |
reads_region.bam value |
| Test-5 |
input: reads_region.bam advanced_options|report_BND: True |
name: value |
reads_region.bam value |
| Test-6 |
input: reads_region.bam parameter_estimation_options|skip_parameter_estimation: True |
name: value |
reads_region.bam value |