Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_seqs/mothur_get_seqs/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_seqs/mothur_get_seqs/1.36.1.0 |
mothur_get_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; ## create symlinks to input datasets ln -s '$accnos' accnos.dat && ln -s '$fasta_in' fasta_in.dat && ln -s '$fastq_in' fastq_in.dat && ln -s '$count_in' count_in.dat && ln -s '$qfile_in' qfile_in.dat && ln -s '$name_in' name_in.dat && ln -s '$group_in' group_in.dat && ln -s '$alignreport_in' alignreport_in.dat && ln -s '$list_in' list_in.dat && ln -s '$taxonomy_in' taxonomy_in.dat && echo 'get.seqs( accnos=accnos.dat, #if $fasta_in: fasta=fasta_in.dat, #end if #if $fastq_in: fastq=fastq_in.dat, #end if #if $count_in: count=count_in.dat, #end if #if $qfile_in: qfile=qfile_in.dat, #end if #if $name_in: name=name_in.dat, #end if #if $group_in: group=group_in.dat, #end if #if $alignreport_in: alignreport=alignreport_in.dat, #end if #if $list_in: list=list_in.dat, #end if #if $taxonomy_in: taxonomy=taxonomy_in.dat, #end if dups=$dups )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
accnos: Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos fasta_in: Mock_S280_L001_R1_001_small.trim.contigs.fasta dups: False savelog: True |
name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos Mock_S280_L001_R1_001_small.trim.contigs.fasta value |
Test-2 |
accnos: Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos fastq_in: Mock_S280_L001_R1_001_small.fastq savelog: True |
name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos Mock_S280_L001_R1_001_small.fastq value |
Test-3 |
accnos: Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos fasta_in: Mock_S280_L001_R1_001_small.trim.contigs.fasta fastq_in: Mock_S280_L001_R1_001_small.fastq dups: False savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos Mock_S280_L001_R1_001_small.trim.contigs.fasta Mock_S280_L001_R1_001_small.fastq value |
Test-4 |
accnos: amazon.bad.accnos count_in: amazon.count_table savelog: True |
name: value name: value |
amazon.bad.accnos amazon.count_table value |