Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0 |
mothur_classify_seqs |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
mothur | 1.39.5 | package |
Additional information about this tool |
set -o pipefail; export TERM=vt100; ## enable mothur to find blast ln -s `dirname \$(which mothur)`/* . && ## create symlinks to input datasets ln -s '$fasta' fasta.dat && ln -s '$alignment.template' alignment.template.dat && ln -s '$tax.taxonomy' tax.taxonomy.dat && ln -s '$count' count.dat && ln -s '$name' name.dat && echo 'classify.seqs( fasta=fasta.dat, reference=alignment.template.dat, taxonomy=tax.taxonomy.dat, method=$classify.method, #if $classify.method == "wang": ksize=$classify.ksize, iters=$classify.iters, cutoff=$classify.cutoff, probs=$classify.probs, #elif $classify.method == "knn": numwanted=$classify.numwanted, search=$classify.search.algorithm, #if $classify.search.algorithm == "kmer": ksize=$classify.search.ksize, #elif $classify.search.algorithm == "blast": match=$classify.search.match, mismatch=$classify.search.mismatch, gapopen=$classify.search.gapopen, gapextend=$classify.search.gapextend, #end if #end if #if $count: count=count.dat, #end if #if $name: name=name.dat, #end if relabund=$relabund, output=$output, printlevel=$printlevel, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | ./mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
fasta: amazon.fasta alignment|template: abrecovery.fasta alignment|source: hist tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source2: hist savelog: True |
name: value name: value name: value name: value |
amazon.fasta abrecovery.fasta abrecovery.pds.wang.taxonomy value |
Test-2 |
fasta: amazon.fasta alignment|template: abrecovery.fasta alignment|source: hist tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source2: hist classify|method: knn savelog: True |
name: value name: value name: value |
amazon.fasta abrecovery.fasta abrecovery.pds.wang.taxonomy value |
Test-3 |
fasta: abrecovery.fasta alignment|template: abrecovery.fasta alignment|source: hist tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source2: hist classify|search|algorithm: blast classify|method: knn savelog: True |
name: value name: value name: value |
abrecovery.fasta abrecovery.pds.wang.taxonomy value |