| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/sansa_annotate/sansa_annotate/0.2.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/sansa_annotate/sansa_annotate/0.2.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/sansa_annotate/sansa_annotate/0.0.8+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/sansa_annotate/sansa_annotate/0.0.7+galaxy0 |
| sansa_annotate |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| sansa | 0.2.2 | package |
| Additional information about this tool |
## initialize
## file format gtf.gz is required
#if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
gzip -c '$type_cond.fg.gtf' > 'db.gtf.gz' &&
#end if
## run
sansa annotate
## sv annotation options
#if $type_cond.type_sel == 's' or $type_cond.type_sel == 'sfg'
--db '$type_cond.s.db'
--bpoffset $type_cond.s.bpoffset
--ratio $type_cond.s.ratio
--strategy '$type_cond.s.strategy'
$type_cond.s.notype
$type_cond.s.nomatch
#end if
## feature and gene annotation options
#if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg'
--gtf 'db.gtf.gz'
--id '$type_cond.fg.id'
--feature '$type_cond.fg.feature'
--distance $type_cond.fg.distance
$type_cond.fg.contained
#end if
## input
'$input'
## postprocessing
2>&1 | tee -a '$out_log'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input: input.vcf type_cond|s|db: db.vcf type_cond|type_sel: s oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.vcf value |
| Test-2 |
input: input.vcf type_cond|s|db: db.vcf type_cond|s|bpoffset: 51 type_cond|s|ratio: 0.79 type_cond|s|strategy: all type_cond|s|notype: True type_cond|s|nomatch: True type_cond|type_sel: s oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.vcf value |
| Test-3 |
input: input.vcf type_cond|fg|gtf: db.gtf type_cond|type_sel: fg oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.gtf value |
| Test-4 |
input: input.vcf type_cond|fg|gtf: db.gtf type_cond|fg|id: gene_id type_cond|fg|feature: exon type_cond|fg|distance: 1001 type_cond|fg|contained: True type_cond|type_sel: fg oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.gtf value |
| Test-5 |
input: input.vcf type_cond|s|db: db.vcf type_cond|fg|gtf: db.gtf type_cond|type_sel: sfg oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.vcf db.gtf value |
| Test-6 |
input: input.vcf type_cond|s|db: db.vcf type_cond|s|bpoffset: 51 type_cond|s|ratio: 0.79 type_cond|s|strategy: all type_cond|s|notype: True type_cond|s|nomatch: True type_cond|fg|gtf: db.gtf type_cond|fg|id: gene_id type_cond|fg|feature: exon type_cond|fg|distance: 1001 type_cond|fg|contained: True type_cond|type_sel: sfg oo|out: ['anno', 'log', 'query'] |
name: value name: value name: value |
input.vcf db.vcf db.gtf value |