Repository revision
9:6f281dc9d01c

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

Consensus.seqs tool metadata
Miscellaneous
Find a consensus sequence for each OTU or phylotype
mothur_consensus_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_consensus_seqs/mothur_consensus_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_consensus_seqs/mothur_consensus_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_consensus_seqs/mothur_consensus_seqs/1.36.1.0
mothur_consensus_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; 

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$count' count.dat &&
#if $perotu.use == "yes":
    ln -s '$perotu.otu' perotu.otu.dat &&
#end if

echo 'consensus.seqs(
    fasta=fasta.dat
    #if $name:
        ,name=name.dat
    #end if
    #if $cutoff:
        ,cutoff=$cutoff
    #end if
    #if $perotu.use == "yes":
        ,list=perotu.otu.dat
        #if $perotu.label:
            ,label=${ str($perotu.label).replace(",","-") }
        #end if
    #end if
    #if $count:
        ,count=count.dat
    #end if
)'
| 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.align_head
savelog: True
name: value
name: value
name: value
amazon.align_head
value
Test-2 fasta: amazon.align_head
perotu|otu: amazon.align_head.list
perotu|use: yes
count: amazon.align_head.count_table
savelog: True
name: value
amazon.align_head
amazon.align_head.list
amazon.align_head.count_table
value