Mercurial > repos > leomrtns > iqtree
changeset 3:a396ccf6079c draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/iqtree"
| author | leomrtns |
|---|---|
| date | Wed, 18 Dec 2019 13:46:22 +0000 |
| parents | 87daf702e477 |
| children | |
| files | iqtree.xml readme.txt |
| diffstat | 2 files changed, 107 insertions(+), 43 deletions(-) [+] |
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--- a/iqtree.xml Thu Sep 05 13:14:43 2019 -0400 +++ b/iqtree.xml Wed Dec 18 13:46:22 2019 +0000 @@ -16,8 +16,8 @@ #end if ## file -#if $general_options.t - -t '$general_options.t' +#if str($initial_tree.mode.tree) == "file" + -t '$initial_tree.mode.t' $tree_parameters.constructing_consensus.con $tree_parameters.constructing_consensus.net #if str($tree_parameters.constructing_consensus.bi) != '' @@ -39,11 +39,27 @@ $tree_parameters.computing_robinson_foulds.rf_all $tree_parameters.computing_robinson_foulds.rf_adj #end if -#end if +#else if str($initial_tree.mode.tree) == "fixed" + -te '$initial_tree.mode.te' +#else if str($initial_tree.mode.tree) == "default" + #if str($initial_tree.mode.ninit) != '' + -ninit '$initial_tree.mode.ninit' + #end if + #if str($initial_tree.mode.sprrad) != '' + -sprrad '$initial_tree.mode.sprrad' + #end if +#else if str($initial_tree.mode.tree) == "fast" + -fast -nbest 1 +#else if str($initial_tree.mode.tree) == "pars" + -t PARS -ninit 2 -nbest 1 +#else + -t BIONJ -ninit 2 -nbest 1 +#end if -## file -#if $general_options.te - -te '$general_options.te' +#if str($initial_tree.mode.tree) in ["fixed", "default", "file"]: + #if str($tree_parameters.tree_search.nbest) != '' + -nbest '$tree_parameters.tree_search.nbest' + #end if #end if #if str($general_options.st) != '' @@ -154,18 +170,11 @@ $modelling_parameters.site_specific_frequency.fmax - -#if str($tree_parameters.tree_search.ninit) != '' - -ninit '$tree_parameters.tree_search.ninit' -#end if - #if str($tree_parameters.tree_search.ntop) != '' -ntop '$tree_parameters.tree_search.ntop' #end if -#if str($tree_parameters.tree_search.nbest) != '' - -nbest '$tree_parameters.tree_search.nbest' -#end if + #if str($tree_parameters.tree_search.nstop) != '' -nstop '$tree_parameters.tree_search.nstop' @@ -175,17 +184,12 @@ -n '$tree_parameters.tree_search.n' #end if -#if str($tree_parameters.tree_search.sprrad) != '' - -sprrad '$tree_parameters.tree_search.sprrad' -#end if - #if str($tree_parameters.tree_search.pers) != '' -pers '$tree_parameters.tree_search.pers' #end if $tree_parameters.tree_search.allnni $tree_parameters.tree_search.djc -$tree_parameters.tree_search.fast ## file #if $tree_parameters.tree_search.g @@ -278,23 +282,77 @@ <section name="general_options" expanded="True" title="General options"> <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/> <param argument="-st" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences"> - <help><![CDATA[ -Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code. -<br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]> - </help> <option value="DNA">DNA</option> <option value="AA">AA</option> <option value="BIN">BIN</option> <option value="MORPH">MORPH</option> <option value="CODON">CODON</option> <option value="NT2AA">NT2AA</option> + <help><![CDATA[ + Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code. + <br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. + You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table). + ]]> + </help> </param> - <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/> - <param argument="-te" type="data" format="nhx" optional="true" label="Like -t but fixing user tree" help="That means, no tree search is performed and IQ-TREE computes the log-likelihood of the fixed user tree."/> <param argument="-seed" type="integer" optional="true" label="Specify a random number seed to reproduce a previous run (leave blank to randomize)"/> <param argument="-keep_ident" type="boolean" truevalue="-keep-ident" falsevalue="" checked="false" label="Keep identical sequences in the alignment" help="By default: IQ-TREE will remove them during the analysis and add them in the end."/> <param argument="-safe" type="boolean" truevalue="-safe" falsevalue="" checked="false" label="Turn on safe numerical mode to avoid numerical underflow for large data sets with many sequences (typically in the order of thousands)" help="This mode is automatically turned on when having more than 2000 sequences."/> </section> + + <section name="initial_tree" expanded="True" title="Input and initial trees"> + <conditional name="mode"> + <param name="tree" type="select" label="Initial tree search"> + <option value="default" selected="true">parsimony using PLL library (default) </option> + <option value="fast">fasttree emulation (option "-fast")</option> + <option value="pars">fast parsimony, using IQTREE internal algorithm (option "-t PARS")</option> + <option value="bionj">bioNJ tree (option "-t BIONJ")</option> + <option value="fixed">fixed tree, no optimisation (option "-te"). Used in e.g. ancestral reconstruction</option> + <option value="file">initial trees from file (option "-t"). Also used for consensus and for tree distance calculations</option> + <help><![CDATA[ + The options for the initial tree estimation are parsimony (default), fast parsimony, fasttree emulation, bioNJ, fixed (no optimisation), and from file. <br/> + The default parsimony estimation is through the PLL library, which is linear on the number of <i>sites</i> and not <i>patterns</i> (so slower than other algorithms). + Notice that this library is also used to populate the "initial parsimony trees" set ("<i>-ninit</i>" below), so keep that in mind. <br/> + + <br/>According to the documentation (see http://www.iqtree.org/doc/Command-Reference#tree-search-parameters), the option "-fast" + "Turn on the fast tree search mode, where IQ-TREE will just construct two starting trees: maximum parsimony and BIONJ, which are then optimized + by nearest neighbor interchange (NNI)." + If you chose fast parsimony, fasttree, or bioNJ, it is assumed that the initial set of trees is two ("-ninit 2") since doing otherwise would defeat the purpose + of avoiding the default PLL.<br/> + <br/>You can also select a tree file as input to IQ_TREE. In most cases this tree file is used as + initial state for optimisation (or as a fixed topology). But in some cases it is used for consensus tree calculation or Robinson-Foulds distances. + There are a few reasons why you should provide trees to IQ-TREE: + <ul> + <li>Through a <b>constrained tree search</b>, where you give a (potentially small, multifurcating) tree which should be respected when searching for optimal trees. + This is given through option <i>"-g"</i>. You use this option when you "know" or want to test a specific grouping of taxa. (Section "Tree search parameters")</li> + <li>Input trees for <b>tree fit comparison</b>, as in section "Tree topology tests" below. IQ-TREE may still do model optimisation, initial tree search, etc. since + it compares the user-provided trees assuming a common model. </li> + <li>Suggest the <b>initial trees</b> (option "<i>-t</i>"). From these, IQ-TREE will start exploring trees (to speed up the tree search in case you already have + good candidate trees). This same command (i.e. same tree file) can also be used for calculating consensus trees or distances between trees. The other options will + inform IQ-TREE how it should use this file (here, the default is to use it as starting tree). </li> + <li>By <b>fixing the tree</b> (option "<i>-te</i>"). This means that IQ-TREE will not try any optimisation with other topologies, and can be used e.g. in ancestral reconstruction. </li> + </ul> + ]]></help> + </param> + <when value="default"> + <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees (default=100)" + help="This value must be strictly higher than the number of best trees to maintain (i.e. higher than 5 under default settings)."/> + <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/> + </when> + <when value="file"> + <param argument="-t" type="data" format="nhx" optional="false" label="Specify a file containing the starting tree for tree search" + help="also used by consensus or distance calculations, if you set the appropriate variables in 'Tree Parameters' below"/> + </when> + <when value="fixed"> + <param argument="-te" type="data" format="nhx" optional="false" label="file with fixed user tree" help="No tree search is performed and IQ-TREE + computes the log-likelihood of the fixed user tree."/> + </when> + <when value="fast"/> + <when value="pars"/> + <when value="bionj"/> + </conditional> + </section> + <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis"> <param argument="-lmap" type="integer" optional="true" label="Specify the number of quartets to be randomly drawn" help="If you specify -lmap ALL, all unique quartets will be drawn, instead."/> <param argument="-lmclust" type="data" format="txt" optional="true" label="Specify a NEXUS file containing taxon clusters (see below for example) for quartet mapping analysis."/> @@ -303,7 +361,12 @@ <section name="modelling_parameters" title="Modelling Parameters"> <section name="automatic_model" expanded="False" title="Automatic model selection"> <conditional name="cond_model" > - <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/> + <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model"> + <help><![CDATA[ + With this option, you can restrict the analysis to a fixed model instead of letting iq-tree select the best one (slow model selection). + Suggestions include "HKY+G" (good compromise speed-performance) or "GTR+G+I" (parameter-rich model). + <br>See http://www.iqtree.org/doc/Substitution-Models for a full list]]> + </help></param> <when value="true"> <param argument="-m" type="text" label="Model"> <sanitizer> @@ -426,25 +489,18 @@ </section> <section name="tree_parameters" title="Tree Parameters"> <section name="tree_search" expanded="False" title="Tree search parameters"> - <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="fast tree search mode"> - <help><![CDATA[ - <br/>Emulates fasttree. According to the documentation (see http://www.iqtree.org/doc/Command-Reference#tree-search-parameters): - <br/>"Turn on the fast tree search mode, where IQ-TREE will just construct two starting trees: maximum parsimony and BIONJ, which are then optimized - by nearest neighbor interchange (NNI). Introduced in version 1.6." - <br/> Some options below may therefore be unused (e.g. the initial number of parsimony trees...) - ]]> - </help> - </param> + <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop + (-nstop and -pers are the most relevant when increasing exploration space, according to IQ_TREE reference manual)"/> + <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI + (-nstop and -pers are the most relevant when increasing exploration space, according to IQ_TREE reference manual)"/> <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides -nstop criterion)." /> - <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/> + <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search (default=5)" + help="This value must be strictly smaller than the number of initial pasimony trees (i.e. less than 100 for default settings)"/> <param argument="-ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/> - <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/> - <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/> - <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/> - <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/> <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/> - <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/> - <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/> + <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree (when generating tree set)" + help="This is independent on how the initial tree/trees were found, and is added to set of initial trees (since it was estimated using likelihood parameters) "/> + <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa. (see https://github.com/Cibiv/IQ-TREE/wiki/Advanced-Tutorial#constrained-tree-search)"/> </section> <section name="single_branch" expanded="False" title="Single branch tests"> <param argument="-alrt" type="integer" optional="true" label="Specify number of replicates (>=1000) to perform SH-like approximate likelihood ratio test (SH-aLRT) (Guindon et al., 2010)" help="If number of replicates is set to 0 (-alrt 0), then the parametric aLRT test (Anisimova and Gascuel 2006) is performed, instead of SH-aLRT."/> @@ -452,7 +508,14 @@ <param argument="-lbp" type="integer" optional="true" label="Specify number of replicates (>=1000) to perform fast local bootstrap probability method (Adachi and Hasegawa, 1996)."/> </section> <section name="tree_topology" expanded="False" title="Tree topology tests"> - <param argument="-z" type="data" format="txt" optional="true" label="Specify a file containing a set of trees" help="IQ-TREE will compute the log-likelihoods of all trees."/> + <param argument="-z" type="data" format="txt" optional="true" label="Specify a file containing a set of trees"> + <help><![CDATA[ + IQ-TREE will compute and compare the log-likelihoods of all trees in this file. It may still search for an optimal tree, in order to find best model and parameters + (unless you fixed those as well). It is strongly suggested to also perform some tests below (like RELL, AU, etc.). See more info at + https://github.com/Cibiv/IQ-TREE/wiki/Advanced-Tutorial#tree-topology-tests + ]]> + </help> + </param> <param argument="-zb" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (>=1000) to perform several tree topology tests for all trees passed via -z" help="The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002)."/> <param argument="-zw" type="boolean" truevalue="-zw" falsevalue="" checked="false" label="Used together with -zb to additionally perform the weighted-KH and weighted-SH tests."/> <param argument="-au" type="boolean" truevalue="-au" falsevalue="" checked="false" label="Used together with -zb to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -zb."/>