Repository revision
10:4d76fba83f24

Repository 'mothur_dist_seqs'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs

Dist.seqs tool metadata
Miscellaneous
Dist.seqs
calculate uncorrected pairwise distances between aligned sequences
mothur_dist_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.36.1.0
mothur_dist_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 '$fasta' fasta.dat &&

echo 'dist.seqs(
    fasta=fasta.dat,
    #if $calc:
        calc=$calc,
    #end if
    countends=$countends,
    #if $cutoff:
        cutoff=$cutoff,
    #end if
    #if $output:
        output=$output,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 fasta: HMP_MOCK.v35.align
savelog: True
name: value
name: value
HMP_MOCK.v35.align
value
Test-2 fasta: HMP_MOCK.v35.align
calc: nogaps
countends: False
cutoff: 0.3
output: lt
savelog: True
name: value
name: value
HMP_MOCK.v35.align
value