Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.36.1.0 |
mothur_count_groups |
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 '$group' group.dat && #if $groupnames.source == "accnos": ln -s '$groupnames.accnos' groupnames.accnos.dat && #end if echo 'count.groups( #if $group.is_of_type("mothur.shared"): shared=group.dat #elif $group.is_of_type("mothur.count_table"): count=group.dat #else: group=group.dat #end if #if $groupnames.source == "groups": #if $groupnames.groups: ,groups=${ str($groupnames.groups).replace(",","-") } #end if #elif $groupnames.source == "accnos": #if $groupnames.accnos: ,accnos=groupnames.accnos.dat #end if #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log && ## parse relevant tool output from logfile to file cat mothur.*.logfile | head -n-7 | sed '1,30d' > '$grp_count'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
group: amazon.an.shared savelog: True |
name: value name: value name: value |
amazon.an.shared value |
Test-2 |
group: amazon.an.shared groupnames|groups: ['forest', 'pasture'] groupnames|source: groups savelog: True |
name: value name: value name: value |
amazon.an.shared value |