Mercurial > repos > iuc > phyml
changeset 3:7157a5b34a68 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
| author | iuc |
|---|---|
| date | Mon, 23 Oct 2023 17:15:37 +0000 |
| parents | 2bf47d57ebb5 |
| children | |
| files | phyml.xml test-data/phylip_phyml_stats.txt |
| diffstat | 2 files changed, 66 insertions(+), 56 deletions(-) [+] |
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--- a/phyml.xml Mon Jun 22 18:37:56 2020 -0400 +++ b/phyml.xml Mon Oct 23 17:15:37 2023 +0000 @@ -1,38 +1,48 @@ -<tool id="phyml" name="PhyML" version="@VERSION@"> - <description>Phylogeny software based on the maximum-likelihood method.</description> +<tool id="phyml" name="PhyML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> + <description>Phylogeny software based on the maximum-likelihood method</description> <macros> - <token name="@VERSION@">3.3.20190909</token> + <token name="@TOOL_VERSION@">3.3.20220408</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> + <xrefs> + <xref type="bio.tools">phyml</xref> + </xrefs> <requirements> - <requirement type="package" version="@VERSION@">phyml</requirement> + <requirement type="package" version="@TOOL_VERSION@">phyml</requirement> </requirements> + <stdio> + <regex source="stdout" match="failed" level="fatal" description="PhyML failed"/> + </stdio> <version_command> - <![CDATA[ phyml --version ]]> + <![CDATA[ phyml --version || true ]]> </version_command> - <command detect_errors="default"> + <command> <![CDATA[ + #import re ##PhyML outputs are based on input path and we need to create outputs in working_dir. - ln -sf '$input' '${input.name}' && - #if $userInputTree: - ln -sf '${$userInputTree}' '${$userInputTree.name}' && + #set input_name = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) + ln -sf '$input' '$input_name' && + #if $userInputTree + #set userInputTree_name = re.sub('[^\s\w\-]', '_', str($userInputTree_name.element_identifier)) + ln -sf '$$userInputTree' '$userInputTree_name' && #end if - phyml --input '${input.name}' - '${phylip_format}' + phyml --input '$input_name' + ${phylip_format} --datatype '${seq.type_of_seq}' --multiple '${nb_data_set}' #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']): --bootstrap '${support_condition.branchSupport}' #else: - --bootstrap '${support_condition.branchSupport.replicate}' + --bootstrap '${support_condition.replicate}' #end if + --model '${seq.model}' #if $seq.type_of_seq == "nt": -t '${seq.tstv}' #end if - --model '${seq.model}' -f '${equi_freq}' --pinv '${prop_invar}' @@ -46,32 +56,32 @@ -o '${optimisationTopology}' #if $userInputTree: - --inputtree '${$userInputTree.name}' + --inputtree '${$userInputTree_name}' #end if #if $numStartSeed != "0": --r_seed '${numStartSeed}' #end if - --no_memory_check > '${output_stdout}' && - grep 'failed' '${output_stdout}' >&2; + --no_memory_check + | tee '${output_stdout}' ]]> </command> <inputs> - <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/> - <param name="phylip_format" type="select" label="Changes interleaved format"> + <param argument="--input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/> + <param argument="--sequential" name="phylip_format" type="select" label="Changes interleaved format"> <option value="">Interleaved</option> <option value="--sequential">Sequential</option> </param> - <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" /> + <param argument="--multiple" name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" /> <conditional name="seq"> - <param name="type_of_seq" type="select" label="Data type"> + <param argument="--datatype name" name="type_of_seq" type="select" label="Data type"> <option value="nt">Nucleic acids</option> <option value="aa">Amino acids</option> </param> <when value="nt"> - <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" /> - <param name="model" type="select" label="Substitution model"> + <param argument="--ts/tv" name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" /> + <param argument="--model" type="select" label="Substitution model"> <option value="HKY85">HKY85</option> <option value="JC69">JC69</option> <option value="K80">K80</option> @@ -82,7 +92,7 @@ </param> </when> <when value="aa"> - <param name="model" type="select" label="Evolution model"> + <param argument="--model" type="select" label="Evolution model"> <option value="LG">LG</option> <option value="WAG">WAG</option> <option value="JTT">JTT</option> @@ -100,45 +110,45 @@ </param> </when> </conditional> - <param name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/> - <param name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model."> + <param argument="--pinvname" name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/> + <param argument="-f" name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model."> <option value="m">ML/Model</option> <option value="e">Empirical</option> </param> - <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" /> - <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/> - <param name="move" type="select" label="Tree topology search"> + <param argument="--nclasses" name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" /> + <param argument="--alpha" name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/> + <param argument="--search" name="move" type="select" label="Tree topology search"> <option value="NNI">NNI (Nearest Neighbor Interchange)</option> <option value="SPR">SPR (Subtree Pruning and Regraphing)</option> <option value="BEST">Best of NNI and SPR</option> </param> - <param name="optimisationTopology" type="select" label="Optimise topology"> + <param argument="-o" name="optimisationTopology" type="select" label="Optimise topology"> <option value="tlr">Tree topology, Branch length, Rate parameter</option> <option value="tl">Tree topology, Branch length</option> <option value="l">Branch length</option> <option value="r">Rate parameter</option> <option value="n">No parameter is optimized</option> </param> - <conditional name="support_condition"> - <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time"> - <option value="0">No bootstrap</option> - <option value="1">Bootstrap</option> - <option value="-1">likelihood aLRT statistics</option> - <option value="-2">likelihood Chi2-based</option> - <option value="-4" selected='true'>SH-like</option> - <option value="-5">Approximate Bayes branch supports</option> - </param> - <when value="0"/> - <when value="-1"/> - <when value="-2"/> - <when value="-4"/> - <when value="-5"/> - <when value="1"> - <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" /> - </when> + <conditional name="support_condition"> + <param argument="--bootstrap" name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time"> + <option value="0">No bootstrap</option> + <option value="1">Bootstrap</option> + <option value="-1">likelihood aLRT statistics</option> + <option value="-2">likelihood Chi2-based</option> + <option value="-4" selected='true'>SH-like</option> + <option value="-5">Approximate Bayes branch supports</option> + </param> + <when value="0"/> + <when value="-1"/> + <when value="-2"/> + <when value="-4"/> + <when value="-5"/> + <when value="1"> + <param argument="--bootstrap" name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" /> + </when> </conditional> - <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/> - <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/> + <param argument="--r_seed" name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/> + <param argument="--inputtree" name="userInputTree" optional="true" type="data" format="nhx" label="Tree file" help="newick format"/> </inputs> <outputs> <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
--- a/test-data/phylip_phyml_stats.txt Mon Jun 22 18:37:56 2020 -0400 +++ b/test-data/phylip_phyml_stats.txt Mon Oct 23 17:15:37 2023 +0000 @@ -1,6 +1,6 @@ oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo - --- PhyML 3.3.20190909 --- + --- PhyML 3.3.20220408 --- http://www.atgc-montpellier.fr/phyml Copyright CNRS - Universite Montpellier oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo @@ -12,17 +12,17 @@ . Number of taxa: 7 . Log-likelihood: -3113.71269 . Unconstrained log-likelihood: -3015.37711 -. Composite log-likelihood: -14534.82403 +. Composite log-likelihood: -14534.82407 . Parsimony: 177 . Tree size: 0.12462 . Discrete gamma model: Yes - Number of classes: 4 - Gamma shape parameter: 0.774 - - Relative rate in class 1: 0.08994 [freq=0.250000] - - Relative rate in class 2: 0.39631 [freq=0.250000] - - Relative rate in class 3: 0.94938 [freq=0.250000] - - Relative rate in class 4: 2.56437 [freq=0.250000] -. Transition/transversion ratio: 2.937995 + - Relative rate in class 1: 0.08995 [freq=0.250000] + - Relative rate in class 2: 0.39633 [freq=0.250000] + - Relative rate in class 3: 0.94939 [freq=0.250000] + - Relative rate in class 4: 2.56433 [freq=0.250000] +. Transition/transversion ratio: 2.937853 . Nucleotides frequencies: - f(A)= 0.28368 - f(C)= 0.21846 @@ -32,7 +32,7 @@ . Run ID: none . Random seed: 1458308600 . Subtree patterns aliasing: no -. Version: 3.3.20190909 +. Version: 3.3.20220408 . Time used: 0h0m0s (0 seconds) oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo