Miscellaneous |
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
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 |