| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_list_seqs/mothur_list_seqs/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_list_seqs/mothur_list_seqs/1.36.1.0 |
| mothur_list_seqs |
| 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 '$search.input' search.input.dat &&
echo 'list.seqs(
#if $search.intype == "fasta":
fasta=search.input.dat
#elif $search.intype == "fastq":
fastq=search.input.dat
#elif $search.intype == "name":
name=search.input.dat
#else if $search.intype == "group":
group=search.input.dat
#elif $search.intype == "alignreport":
alignreport=search.input.dat
#elif $search.intype == "list":
list=search.input.dat
#elif $search.intype == "taxonomy":
taxonomy=search.input.dat
#elif $search.intype == "count":
count=search.input.dat
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
search|input: amazon.fasta search|intype: fasta savelog: True |
name: value name: value |
amazon.fasta value |
| Test-2 |
search|input: amazon.count_table search|intype: count savelog: True |
name: value name: value |
amazon.count_table value |