| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.6.0+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 |
| snippy |
| 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
#import re
#if str( $fastq_input.fastq_input_selector ) == "paired"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
#elif str( $fastq_input.fastq_input_selector ) == "single"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
#elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
#end if
snippy
--outdir '${dir_name}'
--cpus \${GALAXY_SLOTS:-1}
--ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
#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
--mapqual $adv.mapqual
--mincov $adv.mincov
--minfrac $adv.minfrac
--minqual $adv.minqual
#if $adv.rgid
--rgid '$adv.rgid'
#end if
#if $adv.bwaopt
--bwaopt '$adv.bwaopt'
#end if
#if str( $fastq_input.fastq_input_selector ) == "paired"
--R1 '$fastq_input.fastq_input1'
--R2 '$fastq_input.fastq_input2'
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
--R1 '$fastq_input.fastq_input.forward'
--R2 '$fastq_input.fastq_input.reverse'
#elif str( $fastq_input.fastq_input_selector ) == "single"
--se '$fastq_input.fastq_input_single'
#elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
--peil '$fastq_input.fastq_input_interleaved'
#end if
#if "outcon" in str($outputs) and $adv.rename_cons
&& sed -i 's/>.*/>${dir_name}/' '${dir_name}/snps.consensus.fa'
#end if
&& cp -r '${dir_name}' out
&& tar -czf out.tgz '${dir_name}'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference_source|ref_file: reference.fasta reference_source|reference_source_selector: history fastq_input|fastq_input1: a_1.fastq.gz fastq_input|fastq_input2: a_2.fastq.gz fastq_input|fastq_input_selector: paired adv|mincov: 2 adv|minqual: 60 outputs: ['outgff', 'outsum'] |
name: value name: value |
reference.fasta a_1.fastq.gz a_2.fastq.gz value |
| Test-2 |
reference_source|ref_file: reference.fasta reference_source|reference_source_selector: history fastq_input|fastq_input1: b_1.fastq fastq_input|fastq_input2: b_2.fastq fastq_input|fastq_input_selector: paired adv|mincov: 2 adv|minqual: 60 outputs: ['outgff', 'outsum'] |
name: value name: value |
reference.fasta b_1.fastq b_2.fastq value |
| Test-3 |
reference_source|ref_file: reference.fasta reference_source|reference_source_selector: history fastq_input|fastq_input: paired collection fastq_input|fastq_input_selector: paired_collection adv|mincov: 2 adv|minqual: 60 outputs: ['outgff', 'outsum'] |
name: value name: value |
reference.fasta b_1.fastq b_2.fastq value |
| Test-4 |
reference_source|ref_file: reference.fasta reference_source|reference_source_selector: history fastq_input|fastq_input_single: b_2.fastq fastq_input|fastq_input_selector: single adv|mincov: 2 adv|minqual: 60 outputs: ['outgff', 'outsum'] |
name: value name: value |
reference.fasta b_2.fastq value |
| Test-5 |
reference_source|ref_file: test_id reference_source|reference_source_selector: cached fastq_input|fastq_input_single: b_2.fastq fastq_input|fastq_input_selector: single adv|mincov: 2 adv|minqual: 60 outputs: ['outgff', 'outsum'] |
name: value name: value |
b_2.fastq value |