Repository revision
9:470c067fc0a0

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

Make.lefse tool metadata
Miscellaneous
Make.lefse
create a lefse formatted input file from mothur's output files
mothur_make_lefse
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_lefse/mothur_make_lefse/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_make_lefse/mothur_make_lefse/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_lefse/mothur_make_lefse/1.36.1.0
mothur_make_lefse
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 '$otu' otu.dat &&
ln -s '$design' design.dat &&
ln -s '$constaxonomy' constaxonomy.dat &&

echo 'make.lefse(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat,
    #else
        shared=otu.dat,
    #end if
    #if $design:
        design=design.dat,
    #end if
    #if $constaxonomy:
        constaxonomy=constaxonomy.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    scale=$scale
)'
| 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
savelog: True
name: value
name: value
amazon.an.shared
value
Test-2 otu: amazon.an.relabund
label: 0.18
design: toymothur.design2
savelog: True
name: value
name: value
amazon.an.relabund
toymothur.design2
value