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 |
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0+galaxy1 (this tool) |
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 | 4.5.0 | 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 |