Repository revision
10:09bf9e496c64

Repository 'mothur_classify_seqs'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs

Classify.seqs tool metadata
Miscellaneous
Assign sequences to taxonomy
mothur_classify_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
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
    
None
False
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