Repository revision
10:7b96c990a457

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

Cluster.fragments tool metadata
Miscellaneous
Cluster.fragments
Group sequences that are part of a larger sequence
mothur_cluster_fragments
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_fragments/mothur_cluster_fragments/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_cluster_fragments/mothur_cluster_fragments/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_fragments/mothur_cluster_fragments/1.36.1.0
mothur_cluster_fragments
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 '$fasta' fasta.dat &&
ln -s '$names' names.dat &&
ln -s '$count' count.dat &&

echo 'cluster.fragments(
    fasta=fasta.dat,
    diffs=$diffs,
    percent=$percent,
    #if $count:
        count=count.dat,
    #end if
    name=names.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: amazon.fasta
names: amazon1.names
savelog: True
 name: value
name: value
name: value
 amazon.fasta
amazon1.names
value