| Previous changeset 2:2bf47d57ebb5 (2020-06-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5 |
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modified:
phyml.xml test-data/phylip_phyml_stats.txt |
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| diff -r 2bf47d57ebb5 -r 7157a5b34a68 phyml.xml --- a/phyml.xml Mon Jun 22 18:37:56 2020 -0400 +++ b/phyml.xml Mon Oct 23 17:15:37 2023 +0000 |
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| b'@@ -1,38 +1,48 @@\n-<tool id="phyml" name="PhyML" version="@VERSION@">\n- <description>Phylogeny software based on the maximum-likelihood method.</description>\n+<tool id="phyml" name="PhyML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">\n+ <description>Phylogeny software based on the maximum-likelihood method</description>\n <macros>\n- <token name="@VERSION@">3.3.20190909</token>\n+ <token name="@TOOL_VERSION@">3.3.20220408</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n </macros>\n+ <xrefs>\n+ <xref type="bio.tools">phyml</xref>\n+ </xrefs>\n <requirements>\n- <requirement type="package" version="@VERSION@">phyml</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">phyml</requirement>\n </requirements>\n+ <stdio>\n+ <regex source="stdout" match="failed" level="fatal" description="PhyML failed"/>\n+ </stdio>\n <version_command>\n- <![CDATA[ phyml --version ]]>\n+ <![CDATA[ phyml --version || true ]]>\n </version_command>\n- <command detect_errors="default">\n+ <command>\n <![CDATA[\n+ #import re\n ##PhyML outputs are based on input path and we need to create outputs in working_dir.\n- ln -sf \'$input\' \'${input.name}\' &&\n- #if $userInputTree:\n- ln -sf \'${$userInputTree}\' \'${$userInputTree.name}\' && \n+ #set input_name = re.sub(\'[^\\s\\w\\-]\', \'_\', str($input.element_identifier))\n+ ln -sf \'$input\' \'$input_name\' &&\n+ #if $userInputTree\n+ #set userInputTree_name = re.sub(\'[^\\s\\w\\-]\', \'_\', str($userInputTree_name.element_identifier))\n+ ln -sf \'$$userInputTree\' \'$userInputTree_name\' && \n #end if\n \n- phyml --input \'${input.name}\'\n- \'${phylip_format}\'\n+ phyml --input \'$input_name\'\n+ ${phylip_format}\n --datatype \'${seq.type_of_seq}\'\n --multiple \'${nb_data_set}\'\n \n #if (str($support_condition.branchSupport) in [\'0\',\'-1\',\'-2\',\'-4\',\'-5\']):\n --bootstrap \'${support_condition.branchSupport}\'\n #else:\n- --bootstrap \'${support_condition.branchSupport.replicate}\'\n+ --bootstrap \'${support_condition.replicate}\'\n #end if\n \n+ --model \'${seq.model}\'\n #if $seq.type_of_seq == "nt":\n -t \'${seq.tstv}\'\n #end if\n \n- --model \'${seq.model}\'\n -f \'${equi_freq}\'\n --pinv \'${prop_invar}\'\n \n@@ -46,32 +56,32 @@\n -o \'${optimisationTopology}\'\n \n #if $userInputTree:\n- --inputtree \'${$userInputTree.name}\'\n+ --inputtree \'${$userInputTree_name}\'\n #end if\n \n #if $numStartSeed != "0":\n --r_seed \'${numStartSeed}\'\n #end if\n \n- --no_memory_check > \'${output_stdout}\' && \n- grep \'failed\' \'${output_stdout}\' >&2;\n+ --no_memory_check \n+ | tee \'${output_stdout}\' \n ]]>\n </command>\n <inputs>\n- <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>\n- <param name="phylip_format" type="select" label="Changes interleaved format">\n+ <param argument="--input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>\n+ <param argument="--sequential" name="phylip_format" type="select" label="Changes interleaved format">\n <option value="">Interleaved</option>\n <option value="--sequential">Sequential</option>\n </param> \n- <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />\n+ '..b't" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />\n+ <param argument="--alpha" name="gamma" type="text" value="e" label="Parameter of the gamma model" help="\'e\' if you want PhyML to estimate it"/>\n+ <param argument="--search" name="move" type="select" label="Tree topology search">\n <option value="NNI">NNI (Nearest Neighbor Interchange)</option>\n <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>\n <option value="BEST">Best of NNI and SPR</option>\n </param>\n- <param name="optimisationTopology" type="select" label="Optimise topology">\n+ <param argument="-o" name="optimisationTopology" type="select" label="Optimise topology">\n <option value="tlr">Tree topology, Branch length, Rate parameter</option>\n <option value="tl">Tree topology, Branch length</option>\n <option value="l">Branch length</option>\n <option value="r">Rate parameter</option>\n <option value="n">No parameter is optimized</option>\n </param>\n- <conditional name="support_condition">\n- <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">\n- <option value="0">No bootstrap</option>\n- <option value="1">Bootstrap</option>\n- <option value="-1">likelihood aLRT statistics</option>\n- <option value="-2">likelihood Chi2-based</option>\n- <option value="-4" selected=\'true\'>SH-like</option>\n- <option value="-5">Approximate Bayes branch supports</option>\n- </param> \n- <when value="0"/>\n- <when value="-1"/>\n- <when value="-2"/>\n- <when value="-4"/>\n- <when value="-5"/>\n- <when value="1">\n- <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />\n- </when>\n+ <conditional name="support_condition">\n+ <param argument="--bootstrap" name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">\n+ <option value="0">No bootstrap</option>\n+ <option value="1">Bootstrap</option>\n+ <option value="-1">likelihood aLRT statistics</option>\n+ <option value="-2">likelihood Chi2-based</option>\n+ <option value="-4" selected=\'true\'>SH-like</option>\n+ <option value="-5">Approximate Bayes branch supports</option>\n+ </param> \n+ <when value="0"/>\n+ <when value="-1"/>\n+ <when value="-2"/>\n+ <when value="-4"/>\n+ <when value="-5"/>\n+ <when value="1">\n+ <param argument="--bootstrap" name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />\n+ </when>\n </conditional>\n- <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>\n- <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/>\n+ <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"/>\n+ <param argument="--inputtree" name="userInputTree" optional="true" type="data" format="nhx" label="Tree file" help="newick format"/>\n </inputs>\n <outputs>\n <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />\n' |
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| diff -r 2bf47d57ebb5 -r 7157a5b34a68 test-data/phylip_phyml_stats.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 |
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| @@ -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 |