| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_ccode/mothur_chimera_ccode/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_ccode/mothur_chimera_ccode/1.36.1.0 |
| mothur_chimera_ccode |
| 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.template.dat &&
#if $mask_cond.source2 == "history":
ln -s '$mask_cond.input' mask_cond.mask.dat &&
#end if
echo 'chimera.ccode(
fasta=fasta.dat,
reference=alignment.template.dat,
filter=$filter,
#if $mask_cond.source2 == "default":
mask=default,
#elif $mask_cond.source2 == "history":
mask=mask_cond.mask.dat,
#end if
#if int($window) > 0:
window=$window,
#end if
#if int($numwanted) > 0:
numwanted=$numwanted,
#end if
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 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 mask_cond|source2: default window: 100 savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head HMP_MOCK.v35.align value |