Repository revision
9:f6c604b2793e

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

Deunique.seqs tool metadata
Miscellaneous
Return all sequences
mothur_deunique_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_deunique_seqs/mothur_deunique_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_deunique_seqs/mothur_deunique_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_deunique_seqs/mothur_deunique_seqs/1.36.1.0
mothur_deunique_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 '$fasta' fasta.dat &&
ln -s '$names' names.dat &&

 echo 'deunique.seqs(
    #if $inputtype.intype == "countfile":
        count=names.dat,
    #else
        name=names.dat,
    #end if
    fasta=fasta.dat
)'
| 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.unique.fasta
inputtype|names: amazon.unique.names
inputtype|intype: namesfile
savelog: True
name: value
name: value
amazon.unique.fasta
amazon.unique.names
value
Test-2 fasta: amazon.unique.fasta
inputtype|names: amazon_withgroups.count_table
inputtype|intype: countfile
savelog: True
name: value
name: value
name: value
amazon.unique.fasta
amazon_withgroups.count_table
value
Test-3 fasta: amazon.unique.fasta
inputtype|names: amazon.count_table
inputtype|intype: countfile
savelog: True
name: value
name: value
name: value
amazon.unique.fasta
amazon.count_table
value