comparison hyphy_absrel.xml @ 9:cce7b18495e4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"

8:c5533a61ea60

            --branches '$branches'
            --output '$absrel_output'
            #if $log:
                > '$absrel_log'
            #end if
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <expand macro="gencode"/>

            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
    
aBSREL : Adaptive Branch-Site Random Effects Likelihood
=======================================================  
    
What question does this method answer?
--------------------------------------

Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?

Recommended Applications
------------------------

1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences) 

Brief description
-----------------

aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive

Output
------

A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).

For each tested branch the analysis will infer the appropriate number of selective regimes, 
and whether or not there is statistical evidence of positive selection on that branch.

A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)

Further reading

Tool options
------------
::


    --code              Which genetic code to use 

    --branches          Which branches should be tested for selection?
                            All [default] : test all branches
                            
                            Internal : test only internal branches (suitable for 
                            intra-host pathogen evolution for example, where terminal branches
                            may contain polymorphism data)
                            
                            Leaves: test only terminal (leaf) branches
                            
                            Unlabeled: if the Newick string is labeled using the {} notation,
                            test only branches without explicit labels 
                            (see http://hyphy.org/tutorials/phylotree/)

 

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>

9:cce7b18495e4

            --branches '$branches'
            --output '$absrel_output'
            #if $log:
                > '$absrel_log'
            #end if
            ;
        @CATCH_MPIERR@
        ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
        <expand macro="gencode"/>

            <param name="log" value="false"/>
            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

aBSREL : Adaptive Branch-Site Random Effects Likelihood
=======================================================

What question does this method answer?
--------------------------------------

Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?

Recommended Applications
------------------------

1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)

Brief description
-----------------

aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive

Output
------

A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).

For each tested branch the analysis will infer the appropriate number of selective regimes,
and whether or not there is statistical evidence of positive selection on that branch.

A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)

Further reading

Tool options
------------
::


    --code              Which genetic code to use

    --branches          Which branches should be tested for selection?
                            All [default] : test all branches

                            Internal : test only internal branches (suitable for
                            intra-host pathogen evolution for example, where terminal branches
                            may contain polymorphism data)

                            Leaves: test only terminal (leaf) branches

                            Unlabeled: if the Newick string is labeled using the {} notation,
                            test only branches without explicit labels
                            (see http://hyphy.org/tutorials/phylotree/)



    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1093/molbev/msv022</citation>
    </expand>