Repository revision
9:609770e516fa

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

Summary.seqs tool metadata
Miscellaneous
Summary.seqs
Summarize the quality of sequences
mothur_summary_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_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_summary_seqs/mothur_summary_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0
mothur_summary_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 '$count' count.dat &&

echo 'summary.seqs(
    fasta=fasta.dat,
    #if $name:
        name=name.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.fasta
savelog: True
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.fasta
value
Test-2 fasta: amazon.unique.fasta
name: amazon.names
savelog: True
name: value
name: value
amazon.unique.fasta
amazon.names
value
Test-3 fasta: amazon.unique.fasta
count: amazon.count_table
savelog: True
name: value
name: value
amazon.unique.fasta
amazon.count_table
value