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 |