| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/nml/kat_sect/kat_sect/2.3.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/nml/kat_sect/kat_sect/2.3.1 |
| toolshed.g2.bx.psu.edu/repos/nml/kat_sect/kat_sect/1.3.0 |
| kat_sect |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| kat | 2.3.1 | package |
| Additional information about this tool |
cp "$db" db.fasta &&
#if $single_or_paired.type == "single"
ln "$input_se" read.fastq &&
kat sect 'db.fasta'
read.fastq
#elif $single_or_paired.type == "paired"
ln "$single_or_paired.forward_pe" read_1.fastq && ln "$single_or_paired.reverse_pe" read_2.fastq &&
kat sect 'db.fasta'
read_1.fastq read_2.fastq
#else
ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
kat sect 'db.fasta'
read_1.fastq read_2.fastq
#end if
--threads \${GALAXY_SLOTS:-4}
--mer_len $kmer
$keep_counts
-o results
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
keep_counts: False db: db.fasta single_or_paired|input_se: input.fastq |
stats: kat-sect-stats.tsv |
input.fastq db.fasta kat-sect-stats.tsv |
| Test-2 |
keep_counts: True db: db.fasta single_or_paired|input_se: input.fastq |
stats: kat-sect-stats.tsv counts: kat-sect-counts.cvg |
input.fastq db.fasta kat-sect-stats.tsv kat-sect-counts.cvg |