| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0 |
| mothur_make_shared |
| 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 '$intype.otu' intype_otu.dat &&
#if $intype.infile == "otulist":
ln -s '$intype.group' intype_group.dat &&
#end if
echo 'make.shared(
#if $intype.infile == "biom":
biom=intype_otu.dat
#else
#if $intype.group.is_of_type("mothur.groups"):
group=intype_group.dat,
#elif $intype.group.is_of_type("mothur.count_table"):
count=intype_group.dat,
#end if
#if $intype.label:
label=${ str($intype.label).replace(",","-") },
#end if
#if $intype.groups:
groups=${ str($intype.groups).replace(",","-") },
#end if
list=intype_otu.dat
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log &&
## move output files to correct destination
mv mothur.*.logfile "$logfile" &&
#if $intype.infile == 'otulist' and $intype.groups:
mv intype_otu*.groups "$groupout"
#else
mv intype_otu*.shared "$shared"
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
intype|otu: example.biom intype|infile: biom savelog: True |
name: value name: value |
example.biom value |
| Test-2 |
intype|otu: amazon.an.list intype|group: amazon.groups intype|infile: otulist savelog: True |
name: value name: value |
amazon.an.list amazon.groups value |
| Test-3 |
intype|otu: amazon.an.list intype|group: amazon.groups intype|label: ['0.03', '0.05', '0.22'] intype|groups: ['forest', 'pasture'] intype|infile: otulist savelog: True |
name: value name: value |
amazon.an.list amazon.groups value |