Repository revision
9:ddd068a49efe

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

Merge.groups tool metadata
Miscellaneous
Merge.groups
Merge groups in a shared file
mothur_merge_groups
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_groups/mothur_merge_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_merge_groups/mothur_merge_groups/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_groups/mothur_merge_groups/1.36.1.0
mothur_merge_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 '$otu' otu.dat &&
ln -s '$group' group.dat &&
ln -s '$fasta' fasta.dat &&
#if $design.source == "hist":
    ln -s '$design.design_dataset' design_dataset.dat &&
#else:
    ln -s '$generated_design' generated_design.dat &&
#end if

echo 'merge.groups(
    #if $design.source == "hist":
        design=design_dataset.dat
    #else:
        design=generated_design.dat
    #end if
    #if $otu:
        ,shared=otu.dat
    #end if
    #if $group:
        #if $group.is_of_type("mothur.groups"):
            ,group=group.dat
        #elif $group.is_of_type("mothur.count_table"):
            ,count=group.dat
        #end if
    #end if
    #if $fasta:
        ,fasta=fasta.dat
    #end if
    #if $groups:
        ,groups=${ str($groups).replace(",","-") }
    #end if
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
    ,method=$method
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 otu: amazon.an.shared
design|design_dataset: toymothur.design2
design|source: hist
savelog: True
name: value
name: value
amazon.an.shared
toymothur.design2
value
Test-2 otu: amazon.an.shared
label: ['0.05', '0.22', '0.38']
groups: ['forest', 'pasture']
design|design_dataset: toymothur.design2
design|source: hist
savelog: True
name: value
name: value
amazon.an.shared
toymothur.design2
value
Test-3 group: amazon.groups
design|design_dataset: toymothur.design2
design|source: hist
savelog: True
name: value
name: value
amazon.groups
toymothur.design2
value
Test-4 group: amazon_withgroups.count_table
fasta: amazon.fasta
method: median
design|design_dataset: toymothur.design2
design|source: hist
savelog: True
name: value
name: value
amazon_withgroups.count_table
amazon.fasta
toymothur.design2
value
Test-5 otu: amazon.an.shared
design|groupings_0|name: tardis
design|groupings_0|groups: forest
design|groupings_1|name: dalek
design|groupings_1|groups: pasture
design|source: build
savelog: True
name: value
name: value
amazon.an.shared
value