Repository revision
9:c9d3eed082fc

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

Collect.single tool metadata
Miscellaneous
Generate collector's curves for OTUs
mothur_collect_single
toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/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_collect_single/mothur_collect_single/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_collect_single/mothur_collect_single/1.36.1.0
mothur_collect_single
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 &&

echo 'collect.single(
    #if $otu.is_of_type("mothur.rabund"):
        rabund=otu.dat,
    #elif $otu.is_of_type("mothur.sabund"):
        sabund=otu.dat,
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat,
    #elif $otu.is_of_type("mothur.list"):
        list=otu.dat,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    calc=${ str($calc).replace(",","-") },
    abund=$abund,
    freq=$freq
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
&& rm otu.dat  ## don't want this collected into datacollection
    
None
False
Functional tests
name inputs outputs required files
Test-1 otu: amazon.an.list
savelog: True
name: value
amazon.an.list
value
Test-2 otu: amazon.an.sabund
label: ['0.36', '0.38', '0.41']
calc: ['ace', 'bootstrap', 'chao', 'jack', 'sobs', 'simpsoneven', 'shannoneven', 'heip', 'smithwilson', 'bergerparker', 'coverage', 'goodscoverage', 'simpson', 'invsimpson', 'qstat', 'shannon', 'npshannon', 'boneh', 'efron', 'shen', 'solow', 'logseries', 'geometric', 'bstick', 'nseqs']
savelog: True
name: value
amazon.an.sabund
value