| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.0 |
| mothur_chimera_vsearch |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mothur | 1.39.5 | package |
| vsearch | 2.6.0 | package |
| Additional information about this tool |
set -o pipefail; export TERM=vt100;
## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
#if $template.source == "self":
ln -s '$template.count' template.count.dat &&
ln -s '$template.group' template.group.dat &&
#elif $template.source == "names":
ln -s '$template.name' template.name.dat &&
#else:
ln -s '$template.reference' template.reference.dat &&
#end if
echo 'chimera.vsearch(
fasta=fasta.dat,
#if $template.source == "self":
reference=self,
#if float($template.abskew) > 0:
abskew=$template.abskew,
#end if
#if $template.group:
group=template.group.dat,
#end if
#if $template.count:
count=template.count.dat,
#end if
#elif $template.source == "names":
name=template.name.dat,
#else:
reference=template.reference.dat,
#end if
minh=$minh,
mindiv=$mindiv,
xn=$xn,
dn=$dn,
dereplicate=$dereplicate,
mindiffs=$mindiffs,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
2>&1 ## uchime component writes output to stderr
&& cat *accnos
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta: stool_small.unique.fasta template|name: stool_small.names template|source: names savelog: True |
name: value name: value name: value |
stool_small.unique.fasta stool_small.names value |
| Test-2 |
fasta: chimera.fasta template|count: chimera.count_table template|source: self dereplicate: True savelog: True |
name: value name: value name: value name: value |
chimera.fasta chimera.count_table value |
| Test-3 |
fasta: chimera.fasta template|count: chimera.count_table_wogroups template|source: self dereplicate: True savelog: True |
name: value name: value name: value |
chimera.fasta chimera.count_table_wogroups value |
| Test-4 |
fasta: stool_small.unique.fasta template|reference: stool_small.unique.fasta template|source: hist savelog: True |
name: value name: value name: value |
stool_small.unique.fasta value |