| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.36.1.0 |
| mothur_summary_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 'summary.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.list"):
list=otu.dat
#elif $otu.is_of_type("mothur.shared"):
shared=otu.dat,
groupmode=$groupmode
#end if
#if $label:
,label=${ str($label).replace(",","-") }
#end if
#if $calc:
,calc=${ str($calc).replace(",","-") }
#end if
#if $abund:
,abund=$abund
#end if
#if $size:
,size=$size
#end if
#if $subsample.use == 'yes':
#if $subsample.subsample:
,subsample=$subsample.subsample
#else
,subsample=T
#end if
#if $subsample.iters:
,iters=$subsample.iters
#end if
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
#if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode):
&& mv otu.*ave[_-]std.summary otu.ave-std
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
otu: amazon.an.shared subsample|use: yes savelog: True |
name: value name: value |
amazon.an.shared value |
| Test-2 |
otu: amazon.an.shared savelog: True |
name: value name: value |
amazon.an.shared value |
| Test-3 |
otu: amazon.an.shared label: ['0.05', '0.22', '0.32'] 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 name: value |
amazon.an.shared value |
| Test-4 |
otu: amazon.an.shared groupmode: False savelog: True |
name: value |
amazon.an.shared value |
| Test-5 |
otu: amazon.an.rabund subsample|subsample: 10 subsample|iters: 42 subsample|use: yes savelog: True |
name: value name: value name: value |
amazon.an.rabund value |