Repository revision
9:6f08af23888a

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

Degap.seqs tool metadata
Miscellaneous
Degap.seqs
Remove gap characters from sequences
mothur_degap_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_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_degap_seqs/mothur_degap_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.36.1.0
mothur_degap_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 'degap.seqs(
    fasta=fasta.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
savelog: True
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
value