| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_check/mothur_chimera_check/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_check/mothur_chimera_check/1.36.1.0 |
| mothur_chimera_check |
| 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 '$fasta' fasta.dat &&
ln -s '$alignment.reference' alignment.reference.dat &&
#if $svg_cond.svg == "yes":
ln -s '$svg_cond.name' svg.name.dat &&
#end if
echo 'chimera.check(
fasta=fasta.dat,
reference=alignment.reference.dat,
#if $svg_cond.svg == "yes":
svg=yes,
name=svg.name.dat,
#end if
increment=$increment,
ksize=$ksize,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head alignment|reference: HMP_MOCK.v35.align alignment|source: hist savelog: True |
name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head HMP_MOCK.v35.align value |
| Test-2 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head alignment|reference: HMP_MOCK.v35.align alignment|source: hist svg_cond|name: Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny svg_cond|svg: yes savelog: True |
name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head HMP_MOCK.v35.align Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny value |