annotate garli.xml @ 2:681e9bb51cc4 draft default tip

Clean help, fix option descriptions, add genthreshfortopoterm, change filetypes to txt to make it more flexible.

<tool id="Garli" name="Garli" version="2.0" force_history_refresh="True">
  <description> phylogenetic inference using the maximum-likelihood</description>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
## Arguments to the wrapper beyond the config file are just for Galaxy's benefit - all filenames are hardcoded
<command interpreter="python">garli_wrapper.py $garli_conf $best_all_tre $best_tre $log00_log $screen_log </command>
  <inputs>
    <param name="datafname" format="txt" type="data" label="Nexus formated sequence file" force_select="true"/>
    <conditional name="choose_search_type">
        <param name="search_type" type="select" label="Analysis Type">
            <option value="mlsearch" selected="true">ML Search</option>
            <option value="bootstrap">Bootstrap</option>
        </param>
            <when value="mlsearch">
                <param name="searchreps" type="integer" size="4" value="1" label="Number of independent search replicates">
                    <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
                </param>
                <param name="bootstrapreps" type="hidden" value="0" />
                <param name="resampleproportion" type="float"
                    value="1.0" label="Relative size of resample data
                    matrix (0.1-10.0)">
                    <validator type="in_range" message="(0.1-10.0)" min="0.1" max="10.0"/>
                </param>
            </when>
            <when value="bootstrap">
                <param name="searchreps" type="hidden" value="0" />
                <param name="bootstrapreps" type="integer" size="4"
                    value="1" label="Number of bootstrap replicates">
                    <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
                </param>
            </when>
    </conditional>
    <param name="constraintfile" type="data" format="text" label="Constraint file" optional="true"/>
    <conditional name="choose_streefname">
        <param name="streefname_menu" type="select" label="Source of starting tree and/or model">
            <option value="stepwise" selected="true">Stepwise</option>
            <option value="random">Random</option>
            <option value="file">User Tree</option>
        </param>
        <when value="stepwise">
            <param name="streefname" type="hidden" value="stepwise"/>
        </when>
        <when value="random">
            <param name="streefname" type="hidden" value="random"/>
        </when>
        <when value="file">
            <param name="streefname" format="txt" type="data" label="Starting Tree File"/>
        </when>
    </conditional>
    <param name="attachmentspertaxon" size="4" type="integer" value="50"
        label="Attachment branches evaluated per taxon (min=1)" >
        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
    </param>
    <param name="randseed" type="text" size="4" value="-1" label="Random Seed (-1 or
        int)">
        <validator type="in_range" message="(-1 to infinity)" min="-1" max="inf"/>
    </param>
    <param name="availablememory" size="4" value="512" type="integer"
        label="Available Memory"/>
    <param name="refinestart" type="select" label="Perform
        initial rough optimization">
        <option value="1" selected="true">Yes</option>
        <option value="0">No</option>
        </param>
    <param name="outgroup" type="integer" size="20" value="1" label="Outgroup taxa
        numbers"/>
    <param name="collapsebranches" type="select" label="Collapse
        Branches">
        <option value="1" selected="true">Yes</option>
        <option value="0">No</option>
        </param>

        <conditional name="choose_datatype">
        <param name="datatype" type="select" label="Model Type">
            <option value="nucleotide" selected="true">Nucleotide</option>
            <option value="aminoacid">Amino Acid</option>
            <option value="codon-aminoacid">Codon-Amino Acid</option>
            <option value="codon">Codon</option>
        </param>
        <when value="nucleotide">
        <conditional name="choose_ratematrix">
        <param name="ratematrix" type="select" label="Rate Matrix">
            <option value="1rate">1rate</option>
            <option value="2rate">2rate</option>
            <option value="6rate" selected="true">6rate</option>
            <option value="fixed">fixed</option>
            <option value="custom">custom</option>
        </param>
            <when value="1rate" />
            <when value="2rate" />
            <when value="6rate" />
            <when value="fixed" />
            <when value="custom">
                <param name="ratematrix" type="text" size="20" value="(a b a a b a)" label="Custom Rate Matrix"/>
            </when>
        </conditional>
        <param name="statefrequencies" type="select" label="State
        Frequencies">
        <option value="equal">Equal</option>
        <option value="empirical">Empirical</option>
        <option value="estimate" selected="true">Estimate</option>
        <option value="fixed">Fixed</option>
        </param>
        <param name="ratehetmodel" type="select" label="Rate Heterogeneity
        Type">
        <option value="none">None</option>
        <option value="gamma" selected="true">Gamma</option>
        <option value="gammafixed">Gamma Fixed</option>
        </param>
    <param name="numratecats" type="integer" size="2" value="4"
        label="Number of discrete dN/dS categories">
        <validator type="in_range" message="(1-20)" min="1" max="20"/>
    </param>
    <param name="invariantsites" type="select" label="Treatment of
        proportion of invariable sites parameter">
        <option value="none">None</option>
        <option value="estimate" select="true">Estimate</option>
        <option value="fixed">Fixed</option>
    </param>
    </when>
    <when value="aminoacid">
        <param name="ratematrix" type="select" label="Rate Matrix">
            <option value="poisson">Poisson</option>
            <option value="jones" selected="true">Jones</option>
            <option value="dayhoff">Dayhoff</option>
            <option value="wag">WAG</option>
            <option value="mtmam">mtmam</option>
            <option value="mtrev">mtREV</option>
        </param>
        <param name="statefrequences" type="select" label="Equilibrium Base
            Frequences">
            <option value="equal">Equal</option>
            <option value="empirical" selected="true">Empirical</option>
            <option value="estimate">Estimate</option>
            <option value="fixed">Fixed</option>
            <option value="jones">Jones</option>
            <option value="dayhoff">Dayhoff</option>
            <option value="wag">WAG</option>
            <option value="mtmam">mtmam</option>
            <option value="mtrev">mtREV</option>
        </param>
    <param name="numratecats" type="integer" size="2" value="4"
        label="Number of discrete dN/dS categories">
        <validator type="in_range" message="(1-20)" min="1" max="20"/>
    </param>
    <param name="invariantsites" type="select" label="Treatment of
        proportion of invariable sites parameter">
        <option value="none">None</option>
        <option value="estimate" select="true">Estimate</option>
        <option value="fixed">Fixed</option>
    </param>
    </when>
    <when value="codon-aminoacid">
        <param name="ratematrix" type="select" label="Rate Matrix">
            <option value="poisson">Poisson</option>
            <option value="jones" selected="true">Jones</option>
            <option value="dayhoff">Dayhoff</option>
            <option value="wag">WAG</option>
            <option value="mtmam">mtmam</option>
            <option value="mtrev">mtREV</option>
        </param>
        <param name="statefrequences" type="select" label="Equilibrium Base
            Frequences">
            <option value="equal">Equal</option>
            <option value="empirical" selected="true">Empirical</option>
            <option value="estimate">Estimate</option>
            <option value="fixed">Fixed</option>
            <option value="jones">Jones</option>
            <option value="dayhoff">Dayhoff</option>
            <option value="wag">WAG</option>
            <option value="mtmam">mtmam</option>
            <option value="mtrev">mtREV</option>
        </param>
        <param name="geneticcode" type="select" label="Genetic Code">
            <option value="standard" selected="true">Standard</option>
            <option value="vertmito">Vertmito</option>
            <option value="invertmito">Invertmito</option>
        </param>
    </when>
    <when value="codon">
    <conditional name="choose_ratematrix">
        <param name="ratematrix" type="select" label="Rate Matrix">
            <option value="1rate">1rate</option>
            <option value="2rate">2rate</option>
            <option value="6rate" selected="true">6rate</option>
            <option value="fixed">fixed</option>
            <option value="custom">custom</option>
        </param>
            <when value="1rate" />
            <when value="2rate" />
            <when value="6rate" />
            <when value="fixed" />
            <when value="custom">
            <param name="ratematrix" type="text" size="20" value="(a b a a b a)" label="Custom Rate Matrix"/>
        </when>
    </conditional>
    <param name="statefrequencies" type="select" label="State
        Frequencies">
        <option value="equal">Equal</option>
        <option value="empirical" selected="true">Empirical</option>
        <option value="f1x4">F1x4</option>
        <option value="f3x4">F3x4</option>
    </param>
    <param name="ratehetmodel" type="select" label="Rate Heterogeneity
        Type">
        <option value="none" selected="true">None</option>
        <option value="nonsynonymous">Non-synonymous</option>
    </param>
    <param name="numratecats" type="integer" size="2" value="1"
        label="Number of discrete dN/dS categories">
        <validator type="in_range" message="(1-20)" min="1" max="20"/>
    </param>
    <param name="invariantsites" type="hidden" value="none"/>
    <param name="geneticcode" type="select" label="Genetic Code">
        <option value="standard" selected="true">Standard</option>
        <option value="vertmito">Vertmito</option>
        <option value="invertmito">Invertmito</option>
    </param>
    </when>
    </conditional>
    <param name="nindivs" type="integer" size="3" value="4" label="Number of individuals in population">
        <validator type="in_range" message="(2-100)" min="2" max="100"/>
    </param>
    <param name="holdover" type="integer" size="2" value="1" label="Unmutated copies of
        best individual">
        <validator type="in_range" message="(1-99)" min="1" max="99"/>
    </param>
    <param name="selectionintensity" type="float" size="3" value="0.5" label="Strength of
        selection">
        <validator type="in_range" message="(0.1-5.0)" min="0.1" max="5.0"/>
    </param>
    <param name="holdoverpenalty" type="integer" size="3" value="0" label="Fitness
        handicap for best individual">
        <validator type="in_range" message="(0-100)" min="0" max="100"/>
    </param>
    <param name="stopgen" type="integer" size="10" value="5000000" label="Maximum number
        of generations to run">
        <validator type="in_range" message="(0-50000000)" min="0" max="50000000"/>
    </param>
    <param name="stoptime" type="integer" size="10" value="5000000" label="Maximum time to
        run">
        <validator type="in_range" message="(0-50000000)" min="0" max="50000000"/>
    </param>
    <param name="startoptprec" type="float" size="5" value="0.5" label="Starting
        optimization precision">
        <validator type="in_range" message="(0.005-5.0)" min="0.005" max="5.0"/>
    </param>
    <param name="minoptprec" type="float" size="5" value="0.01" label="Minimal
        optimization precision">
        <validator type="in_range" message="(0.001-5.0)" min="0.001" max="5.0"/>
    </param>
    <param name="numberofprecreductions" type="integer" size="3" value="10"
        label="Number of steps down from Start Precision to Minimum Precision"
>
        <validator type="in_range" message="(0-100)" min="0" max="100"/>
    </param>
    <param name="treerejectionthreshold" type="float" size="5" value="50.0"
        label="Tree Rejection Threshold">
        <validator type="in_range" message="(0-500.0)" min="0" max="500.0"/>
    </param>
    <param name="topoweight" type="float" size="10" value="1.0"
        label="Weight on topology mutations">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="modweight" type="float" size="10" value="0.05"
        label="Weight on model parameter mutations">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="brlenweight" type="float" size="10" value="0.2"
        label="Weight on branch-length parameter mutations">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="randnniweight" type="float" size="10" value="0.1"
        label="Weight on NNI topology changes">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="randsprweight" type="float" size="10" value="0.3"
        label="Weight on SPR topology changes">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="limsprweight" type="float" size="10" value="0.6"
        label="Weight on localized SPR topology changes">
        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
    </param>
    <param name="intervallength" type="integer" size="4" value="100"
        label="Interval Length">
        <validator type="in_range" message="(0-1000)" min="0" max="1000"/>
    </param>
    <param name="intervalstostore" type="integer" size="2" value="5"
        label="Number of intervals to store">
        <validator type="in_range" message="(0-1000)" min="0" max="10"/>
    </param>
    <param name="limsprrange" type="integer" size="10" value="6"
        label="Max range for localized SPR topology changes">
        <validator type="in_range" message="(0-1000)" min="0" max="inf"/>
    </param>
    <param name="meanbrlenmuts" type="integer" size="7" value="5"
        label="Mean number of branch lengths to change per mutation">
        <validator type="in_range" message="(0-# of taxa)" min="0" max="10000000000"/>
    </param>
    <param name="gammashapebrlen" type="integer" size="4" value="1000"
        label="Magnitude of branch-length mutations">
        <validator type="in_range" message="(50-2000)" min="50" max="2000"/>
    </param>
    <param name="gammashapemodel" type="integer" size="4" value="1000"
        label="Magnitude of model parameter mutations">
        <validator type="in_range" message="(50-2000)" min="50" max="2000"/>
    </param>
    <param name="uniqueswapbias" type="float" size="4" value="0.1"
        label="Relative weight assigned to already attempted branch swaps"
>
        <validator type="in_range" message="(0.01-1.0)" min="0.01" max="1.0"/>
    </param>
    <param name="distanceswapbias" type="float" size="3" value="1.0"
        label="Relative weight assigned to branch swaps based on locality">
        <validator type="in_range" message="(0.1-10.0)" min="0.1" max="10.0"/>
    </param>
    <param name="genthreshfortopoterm" type="integer" size="5" value="20000"
        label="Number of generations without topology improvement required for termination">
        <validator type="in_range" message="(1-20000)" min="1" max="20000"/>
    </param>
</inputs>
<outputs>
    <data format="nexus" name="best_tre" metadata_source="datafname" from_work_dir="garli.best.tre" label="${tool.name} on ${on_string}: garli.best.tre"/>
    <data format="nexus" name="best_all_tre" metadata_source="datafname" from_work_dir="garli.best.all.tre" label="${tool.name} on ${on_string}: garli.all.best.tre"/>
    <data format="txt" name="garli_conf" from_work_dir="garli.conf" label="${tool.name} on ${on_string}: garli.conf"/>
    <data format="txt" name="log00_log" from_work_dir="garli.log00.log" label="${tool.name} on ${on_string}: garli.log00.log"/>
    <data format="txt" name="screen_log" from_work_dir="garli.screen.log" label="${tool.name} on ${on_string}: garli.screen.log"/>
</outputs>
<configfiles>
<configfile name="garli_conf">
[general]
datafname = ${datafname}
searchreps = ${choose_search_type.searchreps}
bootstrapreps = ${choose_search_type.bootstrapreps}
constraintfile = ${constraintfile}
streefname = ${choose_streefname.streefname}
attachmentspertaxon = ${attachmentspertaxon}
ofprefix = garli
randseed = ${randseed}
availablememory = ${availablememory}
logevery = 10
writecheckpoints = 0
saveevery = 100
refinestart = ${refinestart}
outputeachbettertopology = 0
outputcurrentbesttopology = 0
enforcetermconditions = 1
genthreshfortopoterm = ${genthreshfortopoterm}
scorethreshforterm = 0.05
significanttopochange = 0.01
outputphyliptree = 0
outputmostlyuselessfiles = 0
restart = 0
outgroup = ${outgroup}
resampleproportion = ${choose_search_type.resampleproportion}
inferinternalstateprobs = 0
outputsitelikelihoods = 0
optimizeinputonly = 0
collapsebranches = ${collapsebranches}

[model1]
datatype = ${choose_datatype.datatype}
ratematrix = ${choose_datatype.choose_ratematrix.ratematrix}
statefrequencies = ${choose_datatype.statefrequencies}
ratehetmodel = ${choose_datatype.ratehetmodel}
#if $choose_datatype.numratecats > 0
numratecats = ${choose_datatype.numratecats}
#end if
#if $choose_datatype.invariantsites != ""
invariantsites = ${choose_datatype.invariantsites}
#end if

[master]
nindivs = $nindivs
holdover = $holdover
selectionintensity = $selectionintensity
holdoverpenalty = $holdoverpenalty
stopgen = $stopgen
stoptime = $stoptime

startoptprec = $startoptprec
minoptprec = $minoptprec
numberofprecreductions = $numberofprecreductions
treerejectionthreshold = $treerejectionthreshold
topoweight = $topoweight
modweight = $modweight
brlenweight = $brlenweight
randnniweight = $randnniweight
randsprweight = $randsprweight
limsprweight =  $limsprweight
intervallength = $intervallength
intervalstostore = $intervalstostore
limsprrange = $limsprrange
meanbrlenmuts = $meanbrlenmuts
gammashapebrlen = $gammashapebrlen
gammashapemodel = $gammashapemodel
uniqueswapbias = $uniqueswapbias
distanceswapbias = 1.0
</configfile>
</configfiles>

<help>

**What it does**

GARLI is a program that performs phylogenetic inference using the
maximum-likelihood criterion. Several sequence types are supported,
including nucleotide, amino acid and codon. Version 2.0 adds support
for partitioned models and morphology-like datatypes.

Garli is written and maintained by Derrick Zwickl

Configuration options are adapted from
https://www.nescent.org/wg_garli/GARLI_Configuration_Settings. Please see that
page for more details.

</help>
</tool>