Repository revision
9:abf7c15ecfef

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

Align.seqs tool metadata
Miscellaneous
Align.seqs
Align sequences to a template alignment
mothur_align_seqs
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_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_align_seqs/mothur_align_seqs/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0
mothur_align_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; 

## enable mothur to find blast
ln -s `dirname \$(which mothur)`/* . &&

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&
ln -s '$alignment.reference' alignment.reference.dat &&

echo 'align.seqs(
    fasta=fasta.dat,
    reference=alignment.reference.dat,
    align=$align,
    #if $search.method == "kmer":
        ksize=$search.ksize,
    #else:
        search=$search.method,
    #end if
    #if $scoring.adjust == "yes":
        match=$scoring.match,
        mismatch=$scoring.mismatch,
        gapopen=$scoring.gapopen,
        gapextend=$scoring.gapextend,
    #end if
    #if $reverse.flip == "yes":
        flip=true,
        threshold=$reverse.threshold,
    #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.fasta
alignment|reference: HMP_MOCK.v35.align
alignment|source: history
savelog: True
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
HMP_MOCK.v35.align
value
Test-2 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
alignment|reference: HMP_MOCK.v35.align
alignment|source: history
search|method: kmer
scoring|match: 2
scoring|mismatch: -15
scoring|gapopen: -6
scoring|gapextend: -3
scoring|adjust: yes
savelog: True
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
HMP_MOCK.v35.align
value
Test-3 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
alignment|reference: HMP_MOCK.v35.align
alignment|source: history
search|method: suffix
align: gotoh
scoring|match: 2
scoring|mismatch: -15
scoring|gapopen: -6
scoring|gapextend: -3
scoring|adjust: yes
savelog: True
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
HMP_MOCK.v35.align
value
Test-4 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
alignment|reference: HMP_MOCK.v35.align
alignment|source: history
search|method: blast
align: blast
reverse|threshold: 0.5
reverse|flip: yes
savelog: True
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
HMP_MOCK.v35.align
value
Test-5 fasta: amazon.fasta
alignment|reference: HMP_MOCK.v35.align
alignment|source: history
reverse|threshold: 0.5
reverse|flip: yes
savelog: True
name: value
name: value
name: value
name: value
amazon.fasta
HMP_MOCK.v35.align
value