| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0 |
| mothur_pre_cluster |
| 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 '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
echo 'pre.cluster(
fasta=fasta.dat,
#if $name.is_of_type("mothur.names"):
name=name.dat,
#elif $name.is_of_type("mothur.count_table"):
count=name.dat,
#end if
#if $group:
group=group.dat,
#end if
diffs=$diffs,
match=$match,
mismatch=$mismatch,
gapopen=$gapopen,
gapextend=$gapextend,
topdown=$topdown,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log &&
cat fasta* &&
if [ -f fasta.precluster.map ]; then mv fasta.precluster.map fasta.precluster.fasta.map; fi
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta: amazon.fasta_head name: amazon.head.names savelog: True |
name: value name: value name: value |
amazon.fasta_head amazon.head.names value |
| Test-2 |
fasta: amazon.fasta_head name: amazon.count_table savelog: True |
name: value name: value name: value |
amazon.fasta_head amazon.count_table value |