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 |