comparison hyphy_meme.xml @ 8:3d1f153e2aa1 draft

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

7:74b590fdc6a0

            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            --output '$meme_output'
            > '$meme_log'
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>

        </test>
    </tests>
    <help><![CDATA[
MEME: Mixed Effects Model of Evolution
======================================
    
What question does this method answer?
--------------------------------------

Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
single lineage or subset of lineages, diversifying selection?

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

The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics 
(or balancing selection), including adaptive immune escape by viruses. 
MEME is ideally suited to identify sites under positive selection which 
represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.

MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection. 
MEME is therefore our recommended method if maximum power is desired. 


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

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/)   
                            
     --pvalue           The significance level used to determine significance
     

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pgen.1002764</citation>
    </expand>

8:3d1f153e2aa1

            --code '$gencodeid'
            --branches '$branches'
            --pvalue '$p_value'
            --output '$meme_output'
            > '$meme_log'
            ;
        @CATCH_MPIERR@
    ]]></command>
    <inputs>
        <expand macro="inputs"/>
        <expand macro="gencode"/>
        <expand macro="branches"/>

        </test>
    </tests>
    <help><![CDATA[
MEME: Mixed Effects Model of Evolution
======================================

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

Which site(s) in a gene are subject to pervasive or *episodic*, i.e. only on a
single lineage or subset of lineages, diversifying selection?

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

The phenomenon of pervasive selection is generally most prevalent in pathogen evolution and any biological system influenced by evolutionary arms race dynamics
(or balancing selection), including adaptive immune escape by viruses.
MEME is ideally suited to identify sites under positive selection which
represent candidate sites subject to strong selective pressures across the entire phylogeny or only on parts of the phylogeny.

MEME is the sole method in HyPhy for detecting selection at individual sites that considers both pervasive and episodic selection.
MEME is therefore our recommended method if maximum power is desired.


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

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/)

     --pvalue           The significance level used to determine significance


    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1371/journal.pgen.1002764</citation>
    </expand>