Mercurial > repos > malex > garli
view garli.xml @ 2:681e9bb51cc4 draft default tip
Clean help, fix option descriptions, add genthreshfortopoterm, change filetypes to txt to make it more flexible.
author | malex |
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date | Thu, 05 Jul 2012 17:18:52 -0400 |
parents | 4025ba8b84d6 |
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<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>