Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/1.36.1.0 |
mothur_collect_single |
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 '$otu' otu.dat && echo 'collect.single( #if $otu.is_of_type("mothur.rabund"): rabund=otu.dat, #elif $otu.is_of_type("mothur.sabund"): sabund=otu.dat, #elif $otu.is_of_type("mothur.shared"): shared=otu.dat, #elif $otu.is_of_type("mothur.list"): list=otu.dat, #end if #if $label: label=${ str($label).replace(",","-") }, #end if calc=${ str($calc).replace(",","-") }, abund=$abund, freq=$freq )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log && rm otu.dat ## don't want this collected into datacollection
Functional tests |
name | inputs | outputs | required files |
Test-1 |
otu: amazon.an.list savelog: True |
name: value |
amazon.an.list value |
Test-2 |
otu: amazon.an.sabund label: ['0.36', '0.38', '0.41'] calc: ['ace', 'bootstrap', 'chao', 'jack', 'sobs', 'simpsoneven', 'shannoneven', 'heip', 'smithwilson', 'bergerparker', 'coverage', 'goodscoverage', 'simpson', 'invsimpson', 'qstat', 'shannon', 'npshannon', 'boneh', 'efron', 'shen', 'solow', 'logseries', 'geometric', 'bstick', 'nseqs'] savelog: True |
name: value |
amazon.an.sabund value |