| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/2.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/2.1.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.8 |
| toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7 |
| canu |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| canu | 2.2 | package |
| Additional information about this tool |
#for $counter, $input in enumerate($inputs):
#if $input.ext in ['fastq.gz', 'fasta.gz']
## linking does not work
cp '$input' ./input_${counter}.gz &&
#end if
#end for
canu
#if $stage != 'all':
$stage
#end if
-p canu
-d ./out_dir
#if $s:
-s '$s'
#end if
#if $rawErrorRate:
rawErrorRate=$rawErrorRate
#end if
#if $correctedErrorRate:
correctedErrorRate=$correctedErrorRate
#end if
minReadLength=$minReadLength
minOverlapLength=$minOverlapLength
corOutCoverage=$corOutCoverage
#if $stopOnLowCoverage
stopOnLowCoverage=$stopOnLowCoverage
#end if
#if $minInputCoverage ##and $stage in ["all", "trim-assemble", "assemble"]
minInputCoverage=$minInputCoverage
#end if
contigFilter='
${contigFilter.minReads}
${contigFilter.minLength}
${contigFilter.singleReadSpan}
${contigFilter.lowCovSpan}
${contigFilter.lowCovDepth}
'
genomeSize='$genomeSize'
minThreads=\${GALAXY_SLOTS:-4}
maxThreads=\${GALAXY_SLOTS:-4}
redMemory=\${GALAXY_MEMORY_MB:-6144}M
redThreads=\${GALAXY_SLOTS:-4}
obtovlThreads=\${GALAXY_SLOTS:-4}
utgovlThreads=\${GALAXY_SLOTS:-4}
batThreads=\${GALAXY_SLOTS:-4}
batMemory=\${GALAXY_MEMORY_MB:-6144}M
cormhapMemory=\${GALAXY_MEMORY_MB:-6144}M
obtovlMemory=\${GALAXY_MEMORY_MB:-6144}M
utgovlMemory=\${GALAXY_MEMORY_MB:-6144}M
corThreads=\${GALAXY_SLOTS:-4}
corMemory=\${GALAXY_MEMORY_MB:-6144}M
cnsThreads=\${GALAXY_SLOTS:-4}
cnsMemory=\${GALAXY_MEMORY_MB:-6144}M
oeaMemory=\${GALAXY_MEMORY_MB:-6144}M
oeaThreads=\${GALAXY_SLOTS:-4}
merylThreads=\${GALAXY_SLOTS:-4}
merylMemory=\${GALAXY_MEMORY_MB:-6144}M
corovlThreads=\${GALAXY_SLOTS:-4}
corovlMemory=\${GALAXY_MEMORY_MB:-6144}M
useGrid=false
#for $haplotype in $haplotypes:
-haplotype${haplotype.haplotype_name} '${haplotype.haplotype_input}'
#end for
$technology
#if $processing:
$processing
#end if
#for $counter, $input in enumerate($inputs):
#if $input.ext in ['fastq.gz', 'fasta.gz']
./input_${counter}.gz
#else:
'$input'
#end if
#end for
2>&1
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputs: ecoli-reads.fasta technology: -nanopore genomeSize: 20k minReadLength: 2000 minInputCoverage: 1 stopOnLowCoverage: 1 |
name: value name: value name: value name: value name: value |
ecoli-reads.fasta value |
| Test-2 |
inputs: ecoli-reads.fasta technology: -nanopore genomeSize: 20k rawErrorRate: 0.2 correctedErrorRate: 0.05 minReadLength: 2000 minOverlapLength: 800 minInputCoverage: 1 corOutCoverage: 2 stopOnLowCoverage: 1 |
name: value name: value name: value name: value name: value |
ecoli-reads.fasta value |
| Test-3 |
inputs: ecoli-reads.fasta technology: -nanopore stage: -correct genomeSize: 20k minReadLength: 2500 stopOnLowCoverage: 1 |
name: value name: value |
ecoli-reads.fasta value |
| Test-4 |
inputs: ecoli-reads.fasta technology: -nanopore processing: -corrected stage: -trim genomeSize: 0.01m minReadLength: 500 |
name: value |
ecoli-reads.fasta value |