| 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 |