Repository revision
35:ec783806a5c3

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

HyPhy-FEL tool metadata
Miscellaneous
HyPhy-FEL
Fixed Effects Likelihood
hyphy_fel
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/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_fel/hyphy_fel/2.5.47+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.36+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.31+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.31+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.30+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.29+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.26+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.25+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.24+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.23+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.21+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.17+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.15+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.14+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.12+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.11+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.7+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.5.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_fel/hyphy_fel/2.3.14+galaxy0
hyphy_fel
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
    
        \${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI fel
            --alignment ./$input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
    
            --code '$gencodeid'
            
        #if $branch_cond.branch_sel == 'specify':
            --branches '$branch_cond.branch_label'
        #else:
            --branches $branch_cond.branch_sel
        #end if
        
    
            --srv '$include_srv'
            --pvalue '$p_value'
            
            #if $resample:
                --resample $resample
            #end if
        
    
            --precision $precision
            $ci
            --output '$fel_output'
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
    
    
None
False
Functional tests
name inputs outputs required files
Test-1 input_file: absrel-in1.fa
input_nhx: absrel-in1.nhx
name: value
absrel-in1.fa
absrel-in1.nhx
value
Test-2 input_file: absrel-in1.fa
input_nhx: absrel-in1.nhx
ci: True
precision: reduced
name: value
absrel-in1.fa
absrel-in1.nhx
value