Repository revision
11:e7a88b8551ff

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

Chop.seqs tool metadata
Miscellaneous
Chop.seqs
Trim sequences to a specified length
mothur_chop_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chop_seqs/mothur_chop_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_chop_seqs/mothur_chop_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chop_seqs/mothur_chop_seqs/1.36.1.0
mothur_chop_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 '$fasta' fasta.dat &&
ln -s '$name' name.dat &&
ln -s '$group' group.dat &&
ln -s '$count' count.dat &&

echo 'chop.seqs(
    fasta=fasta.dat,
    numbases=$numbases,
    keep=$keep,
    countgaps=$countgaps,
    short=$short,
    #if $name:
        name=name.dat,
    #end if
    #if $group:
        group=group.dat,
    #end if
    #if $count:
        count=count.dat,
    #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: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
name: Mock_S280_L001_R1_001_small.trim.contigs.good.names
savelog: True
 name: value
name: value
 Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
Mock_S280_L001_R1_001_small.trim.contigs.good.names
value