Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_sharedseqs/mothur_get_sharedseqs/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_sharedseqs/mothur_get_sharedseqs/1.36.1.0 |
mothur_get_sharedseqs |
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 '$infile.otu' infile_otu.dat && #if $infile.intype == "in_listgroup": ln -s '$infile.group' infile.group.dat && ln -s '$infile.fasta' infile_fasta.dat && ln -s '$count_in' count_in.dat && #end if echo 'get.sharedseqs( #if $infile.intype == "in_listgroup": list=infile_otu.dat #if $group: ,group=infile.group.dat #elif $count_in: ,count=count_in.dat #end if #if $infile.fasta: ,fasta=infile_fasta.dat #end if #else shared=infile_otu.dat #end if #if $infile.label: ,label=${ str($infile.label).replace(",","-") } #end if #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups: ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") } #end if #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups: ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") } #end if #if $output: ,output=$output #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
infile|otu: amazon.an.shared infile|seqsfrom|selection: shared infile|intype: in_shared savelog: True |
name: value |
amazon.an.shared value |
Test-2 |
infile|otu: amazon.an.list infile|group: amazon.groups infile|intype: in_listgroup savelog: True |
name: value |
amazon.an.list amazon.groups value |
Test-3 |
infile|otu: amazon.an.shared infile|label: ['0.03', '0.33', '0.41'] infile|seqsfrom|groups: ['forest', 'pasture'] infile|seqsfrom|selection: shared infile|intype: in_shared savelog: True |
name: value |
amazon.an.shared value |
Test-4 |
infile|otu: amazon.an.shared infile|seqsfrom|groups: pasture infile|seqsfrom|selection: unique infile|intype: in_shared savelog: True |
name: value |
amazon.an.shared value |
Test-5 |
infile|otu: amazon.an.shared infile|intype: in_shared output: accnos savelog: True |
name: value |
amazon.an.shared value |
Test-6 |
infile|otu: amazon.an.list infile|group: amazon.groups infile|fasta: amazon.fasta infile|intype: in_listgroup savelog: True |
name: value |
amazon.an.list amazon.groups amazon.fasta value |