Repository revision
2:bb1847435ec1

Repository 'clustalomega'

Clustal Omega tool metadata
Miscellaneous
multiple sequence alignment program for proteins
clustalomega
toolshed.g2.bx.psu.edu/repos/clustalomega/clustalomega/clustalomega/1.0.2
1.0.2
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/clustalomega/clustalomega/clustalomega/1.0.2 (this tool)
toolshed.g2.bx.psu.edu/repos/clustalomega/clustalomega/clustalomega/0.2
clustalomega
Requirements (dependencies defined in the <requirements> tag set)
No requirements defined
Additional information about this tool
hide_stderr.py clustalo --force --threads=1 --maxnumseq=300000 --maxseqlen=15000 -o $output -l $outlog -v 
#if ($basicmode.mode=="mode1")
 -i $input
#elif ($basicmode.mode=="mode2")
 --profile1 $profile1 --profile2 $profile2
#elif ($basicmode.mode=="mode3")
 -i $input --profile1 $profile
#elif ($basicmode.mode=="mode4")
 -i $input --hmm-in=$hmm
#end if
#if($advanced.options=="true")
    #if ($advanced.dealign.value=="Yes")
     --dealign
    #end if
    #if ($advanced.mbed.value=="Yes")
     --full
    #end if
    #if ($advanced.iteration.iteroptions =="true")
        --iter $advanced.iteration.iters
        #if ($advanced.iteration.mbediter.value=="Yes")
         --full-iter
        #end if
        #if ($advanced.iteration.separateiters.separateiteroptions =="true")
         --max-guidetree-iterations=$advanced.iteration.separateiters.gtiters
         --max-hmm-iterations=$advanced.iteration.separateiters.hmmiters
        #end if
    #end if
#end if
#if ($dotree.value=="Yes")
 --guidetree-out=$outtree
#end if

python
False
False
Functional tests
name inputs outputs required files
Test-1 mode: mode1
input: clustalo_unaligned_all.fasta
outname: test_output
options: false
output: clustalo_test1_out.fasta
clustalo_unaligned_all.fasta
clustalo_test1_out.fasta
Test-2 mode: mode2
profile1: clustalo_aligned1.fasta
profile2: clustalo_aligned2.fasta
outname: test_output
options: false
output: clustalo_profileprofile.fasta
clustalo_aligned1.fasta
clustalo_aligned2.fasta
clustalo_profileprofile.fasta