Miscellaneous |
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
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 |