| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_access/cnvkit_access/0.9.12+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_access/cnvkit_access/0.9.11+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_access/cnvkit_access/0.9.11+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_access/cnvkit_access/0.9.10+galaxy0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/cnvkit_access/cnvkit_access/0.9.10+galaxy0 |
| cnvkit_access |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| cnvkit | 0.9.12 | package |
| samtools | 1.21 | package |
| Additional information about this tool |
#import re
ln -s '$fa_fname' ./genome.fasta &&
#if $exclude
#set $names = []
#set $x=1
#for $x, $exc in enumerate($exclude):
#set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier)
#set $name = $name_base
#silent $names.append( $name )
ln -s '$exc' ${name}.bed &&
#end for
#end if
cnvkit.py access
./genome.fasta
#if $exclude
#for $name in $names:
--exclude ${name}.bed
#end for
#end if
#if str($min_gap_size)
--min-gap-size $min_gap_size
#end if
--output access-excludes.bed
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fa_fname: genome.fasta min_gap_size: 2500 exclude: excludes.bed |
name: value |
genome.fasta excludes.bed value |
| Test-2 |
fa_fname: genome.fasta min_gap_size: 2500 exclude: ['excludes.bed', 'excludes_1.bed'] |
name: value |
genome.fasta excludes.bed excludes_1.bed value |