Repository revision
9:408650f291f7

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

Parse.list tool metadata
Miscellaneous
Parse.list
Generate a List file for each group
mothur_parse_list
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parse_list/mothur_parse_list/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_parse_list/mothur_parse_list/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parse_list/mothur_parse_list/1.36.1.0
mothur_parse_list
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 '$count' count.dat &&

echo 'parse.list(
    list=otu.dat,
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $count:
        count=count.dat,
    #end if
    group=group.dat
)'
| 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.list
group: amazon.groups
savelog: True
name: value
amazon.an.list
amazon.groups
value
Test-2 otu: amazon.an.list
group: amazon.groups
label: ['0.03', '0.05']
savelog: True
name: value
amazon.an.list
amazon.groups
value