| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.6.0+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.5.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.5+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.5+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.4.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/4.3.6 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2 |
| snippy_core |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| snippy | 4.6.0 | package |
| tar | 1.32 | package |
| Additional information about this tool |
#if $reference_source.reference_source_selector == 'history'
#if $reference_source.ref_file.is_of_type("fasta")
ln -sf '$reference_source.ref_file' 'ref.fna' &&
#elif $reference_source.ref_file.is_of_type("genbank")
ln -sf '$reference_source.ref_file' 'ref.gbk' &&
#end if
#elif $reference_source.reference_source_selector == 'cached'
ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
#end if
mkdir 'snippy_dirs' && cd 'snippy_dirs' &&
#for $indir in $indirs
tar -xf '$indir' -C . &&
#end for
cd - &&
snippy-core
#if $reference_source.reference_source_selector == 'history'
#if $reference_source.ref_file.is_of_type("fasta")
--ref 'ref.fna'
#elif $reference_source.ref_file.is_of_type("genbank")
--ref 'ref.gbk'
#end if
#elif $reference_source.reference_source_selector == 'cached'
--ref 'ref.fna'
#end if
snippy_dirs/*
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
indirs: ['a.tgz', 'b.tgz', 'c.tgz'] reference_source|ref_file: reference.fasta reference_source|reference_source_selector: history outputs: outtxt |
name: value |
a.tgz b.tgz c.tgz reference.fasta value |
| Test-2 |
indirs: ['a.tgz', 'b.tgz', 'c.tgz'] reference_source|ref_file: test_id reference_source|reference_source_selector: cached outputs: outtxt |
name: value |
a.tgz b.tgz c.tgz value |