| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_tax/mothur_summary_tax/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_tax/mothur_summary_tax/1.36.1.0 |
| mothur_summary_tax |
| 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 '$tax.taxonomy' tax.taxonomy.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
ln -s '$count' count.dat &&
echo 'summary.tax(
taxonomy=tax.taxonomy.dat,
#if $name:
name=name.dat,
#end if
#if $group:
group=group.dat,
#end if
#if $count:
count=count.dat,
#end if
relabund=$relabund,
threshold=$threshold,
output=$output,
printlevel=$printlevel
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist savelog: True |
name: value name: value |
abrecovery.pds.wang.taxonomy value |
| Test-2 |
tax|taxonomy: abrecovery.pds.wang.taxonomy tax|source: hist savelog: True |
name: value name: value |
abrecovery.pds.wang.taxonomy value |