Repository revision
9:03c86648a52e

Repository 'mothur_count_groups'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups

Count.groups tool metadata
Miscellaneous
Count.groups
counts the number of sequences represented by a specific group or set of groups
mothur_count_groups
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
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'
    
None
False
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