Repository revision
34:5eb9d7217640

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

HyPhy-RELAX tool metadata
Miscellaneous
HyPhy-RELAX
Detect relaxed selection in a codon-based phylogenetic framework
hyphy_relax
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/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_relax/hyphy_relax/2.5.47+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.36+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.36+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.31+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.31+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.30+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.29+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.26+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.25+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.24+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.23+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.21+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.17+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.15+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.14+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.12+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.11+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.7+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/hyphy_relax/hyphy_relax/2.5.0+galaxy0
hyphy_relax
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
    
        export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
        hyphy relax
            --alignment ./$input_file
            
            #if $input_nhx:
                --tree input.nhx
            #end if
        
    
            --models '$models'
            --code '$gencodeid'
            --test '$test'
            #if $reference:
                --reference '$reference'
            #end if
            
        #if $advanced.srv_options == 'specify':
            --grid-size $advanced.grid_size
            --starting-points $advanced.starting_points
            --syn-rates $advanced.syn_rates
            --rates $advanced.rates
            --srv $advanced.srv
            #if $advanced.save_alternative_model:
                --save-fit alternative_model.nhx
            #end if
        #end if
    
            --output '$relax_output'
        
        ; EC=\$? ; [[ -f errors.* ]] && cat errors.* >&2 ; exit \$EC
    
    
None
False
Functional tests
name inputs outputs required files
Test-1 input_file: relax-in1.fa
input_nhx: relax-in1.nhx
test: TEST
name: value
relax-in1.fa
relax-in1.nhx
value
Test-2 input_file: relax-in2.nex
test: PR
advanced|srv: False
advanced|save_alternative_model: True
advanced|srv_options: specify
name: value
relax-in2.nex
value