Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0 |
mothur_align_seqs |
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; ## enable mothur to find blast ln -s `dirname \$(which mothur)`/* . && ## create symlinks to input datasets ln -s '$fasta' fasta.dat && ln -s '$alignment.reference' alignment.reference.dat && echo 'align.seqs( fasta=fasta.dat, reference=alignment.reference.dat, align=$align, #if $search.method == "kmer": ksize=$search.ksize, #else: search=$search.method, #end if #if $scoring.adjust == "yes": match=$scoring.match, mismatch=$scoring.mismatch, gapopen=$scoring.gapopen, gapextend=$scoring.gapextend, #end if #if $reverse.flip == "yes": flip=true, threshold=$reverse.threshold, #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.fasta alignment|reference: HMP_MOCK.v35.align alignment|source: history savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta HMP_MOCK.v35.align value |
Test-2 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta alignment|reference: HMP_MOCK.v35.align alignment|source: history search|method: kmer scoring|match: 2 scoring|mismatch: -15 scoring|gapopen: -6 scoring|gapextend: -3 scoring|adjust: yes savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta HMP_MOCK.v35.align value |
Test-3 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta alignment|reference: HMP_MOCK.v35.align alignment|source: history search|method: suffix align: gotoh scoring|match: 2 scoring|mismatch: -15 scoring|gapopen: -6 scoring|gapextend: -3 scoring|adjust: yes savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta HMP_MOCK.v35.align value |
Test-4 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta alignment|reference: HMP_MOCK.v35.align alignment|source: history search|method: blast align: blast reverse|threshold: 0.5 reverse|flip: yes savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta HMP_MOCK.v35.align value |
Test-5 |
fasta: amazon.fasta alignment|reference: HMP_MOCK.v35.align alignment|source: history reverse|threshold: 0.5 reverse|flip: yes savelog: True |
name: value name: value name: value name: value |
amazon.fasta HMP_MOCK.v35.align value |