Repository revision
35:1b893cdead55

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

HyPhy-FUBAR tool metadata
Miscellaneous
HyPhy-FUBAR
Fast Unconstrained Bayesian AppRoximation
hyphy_fubar
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.47+galaxy0
2.5.47+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.47+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.36+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.31+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.31+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.30+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.29+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.26+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.25+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.24+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.23+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.21+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.17+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.15+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.14+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.12+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.11+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.7+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.5.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fubar/hyphy_fubar/2.3.14+galaxy0
hyphy_fubar
Requirements (dependencies defined in the <requirements> tag set)
name version type
hyphy 2.5.47 package
Additional information about this tool
#if $input_nhx is not None:
            ln -s '$input_nhx' input.nhx &&
        #end if
        ln -s '$input_file' input.$input_file.extension &&
        #set $input_file = 'input.%s' % $input_file.extension
    
        ln -s '$fubar_output' ${input_file}.FUBAR.json &&
        hyphy fubar
            --alignment ./$input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
    
            --code '$gencodeid'
            --method '$posteriorEstimationMethod.method'
            --grid '$grid_points'
            
            #if $posteriorEstimationMethod.method != "Variational-Bayes"
                --chains '$posteriorEstimationMethod.chains'
                --chain-length '$posteriorEstimationMethod.chain_length'
                --burn-in '$posteriorEstimationMethod.samples'
                --samples '$posteriorEstimationMethod.samples_per_chain'
            #end if
    
            --concentration_parameter '$concentration'
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
None
False
Functional tests
name inputs outputs required files
Test-1 input_file: fubar-in1.fa.gz
input_nhx: fubar-in1.nhx
posteriorEstimationMethod|method: Variational-Bayes
 name: value
 fubar-in1.fa.gz
fubar-in1.nhx
value