Mercurial > repos > iuc > raxml
changeset 2:a4b71be30c3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
| author | iuc |
|---|---|
| date | Mon, 02 Dec 2019 07:52:10 -0500 |
| parents | ba29b5e2a4be |
| children | 14eb2acf30e3 |
| files | raxml.py raxml.xml test-data/RAxML_parsimonyTree.galaxy.multi |
| diffstat | 3 files changed, 8 insertions(+), 104 deletions(-) [+] |
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--- a/raxml.py Tue Jun 27 16:27:39 2017 -0400 +++ b/raxml.py Mon Dec 02 07:52:10 2019 -0500 @@ -39,8 +39,6 @@ for filename in runfiles: if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): with open(filename, 'r') as infile: - filename_line = "%s\n" % filename - outfile.write(filename_line) for line in infile: outfile.write(line) # Parsimony Trees @@ -48,8 +46,6 @@ for filename in runfiles: if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): with open(filename, 'r') as infile: - filename_line = "%s\n" % filename - outfile.write(filename_line) for line in infile: outfile.write(line) # Results @@ -57,8 +53,6 @@ for filename in runfiles: if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): with open(filename, 'r') as infile: - filename_line = "%s\n" % filename - outfile.write(filename_line) for line in infile: outfile.write(line) # Multiple Model Partition Files @@ -71,8 +65,6 @@ for filename in files: if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): with open(filename, 'r') as infile: - filename_line = "%s\n" % filename - outfile.write(filename_line) for line in infile: outfile.write(line) else: @@ -87,8 +79,6 @@ for filename in files: if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): with open(filename, 'r') as infile: - filename_line = "%s\n" % filename - outfile.write(filename_line) for line in infile: outfile.write(line) else:
--- a/raxml.xml Tue Jun 27 16:27:39 2017 -0400 +++ b/raxml.xml Mon Dec 02 07:52:10 2019 -0500 @@ -1,7 +1,8 @@ -<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4"> +<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1"> <description>- Maximum Likelihood based inference of large phylogenetic trees</description> <requirements> <requirement type="package" version="8.2.4">raxml</requirement> + <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 @@ -447,8 +448,8 @@ <param name="infile" value="dna.phy"/> <param name="model_type" value="nucleotide"/> <param name="base_model" value="GTRCAT"/> - <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" /> - <output name="bestTree"> + <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" /> + <output name="bestTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Frog" /> </assert_contents> @@ -460,14 +461,13 @@ <param name="model_type" value="nucleotide"/> <param name="base_model" value="GTRCAT"/> <param name="number_of_runs" value="5"/> - <output name="parsimonyTree"> + <output name="parsimonyTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Chicken" /> - <has_text_matching expression="RUN.4" /> </assert_contents> </output> - <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/> - <output name="bestTree"> + <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx"/> + <output name="bestTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Whale" /> </assert_contents>
--- a/test-data/RAxML_parsimonyTree.galaxy.multi Tue Jun 27 16:27:39 2017 -0400 +++ b/test-data/RAxML_parsimonyTree.galaxy.multi Mon Dec 02 07:52:10 2019 -0500 @@ -1,87 +1,1 @@ - - -Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" - - - -This is RAxML version 8.2.4 released by Alexandros Stamatakis on October 02 2015. - -With greatly appreciated code contributions by: -Andre Aberer (HITS) -Simon Berger (HITS) -Alexey Kozlov (HITS) -Kassian Kobert (HITS) -David Dao (KIT and HITS) -Nick Pattengale (Sandia) -Wayne Pfeiffer (SDSC) -Akifumi S. Tanabe (NRIFS) - -Alignment has 34 distinct alignment patterns - -Proportion of gaps and completely undetermined characters in this alignment: 0.00% - -RAxML rapid hill-climbing mode - -Using 1 distinct models/data partitions with joint branch length optimization - - -Executing 5 inferences on the original alignment using 5 distinct randomized MP trees - -All free model parameters will be estimated by RAxML -ML estimate of 25 per site rate categories - -Likelihood of final tree will be evaluated and optimized under GAMMA - -GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units - -Partition: 0 -Alignment Patterns: 34 -Name: No Name Provided -DataType: DNA -Substitution Matrix: GTR - - - - -RAxML was called as follows: - -raxmlHPC -s /tmp/tmpS1corm/files/000/dataset_7.dat -n galaxy -m GTRCAT -N 5 -f d -p 1234567890 - - -Partition: 0 with name: No Name Provided -Base frequencies: 0.325 0.288 0.168 0.218 - -Inference[0]: Time 0.216205 CAT-based likelihood -318.296661, best rearrangement setting 5 -alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 156.924095 909.973305 698.798586 49.826281 1854.008494 1.000000 -Inference[1]: Time 0.156515 CAT-based likelihood -320.216706, best rearrangement setting 5 -alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 984.611489 1694.475132 1327.909793 133.166551 5344.045057 1.000000 -Inference[2]: Time 0.168518 CAT-based likelihood -317.720618, best rearrangement setting 5 -alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 467.628294 1755.581565 1080.117186 84.613232 3889.913949 1.000000 -Inference[3]: Time 0.151635 CAT-based likelihood -320.856852, best rearrangement setting 5 -alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 951.225250 1754.836760 1010.717630 104.250644 4976.305821 1.000000 -Inference[4]: Time 0.148819 CAT-based likelihood -320.068842, best rearrangement setting 5 -alpha[0]: 1.000000 rates[0] ac ag at cg ct gt: 1216.938988 2115.384600 1728.203983 157.161613 6782.996281 1.000000 - - -Conducting final model optimizations on all 5 trees under GAMMA-based models .... - -Inference[0] final GAMMA-based Likelihood: -378.273666 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.0 -Inference[1] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.1 -Inference[2] final GAMMA-based Likelihood: -377.272824 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.2 -Inference[3] final GAMMA-based Likelihood: -377.004321 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.3 -Inference[4] final GAMMA-based Likelihood: -378.202304 tree written to file /tmp/tmpS1corm/job_working_directory/000/4/RAxML_result.galaxy.RUN.4 - - -Starting final GAMMA-based thorough Optimization on tree 3 likelihood -377.004321 .... - -Final GAMMA-based Score of best tree -377.004321 - -Program execution info written to /tmp/tmpS1corm/job_working_directory/000/4/RAxML_info.galaxy -Best-scoring ML tree written to: /tmp/tmpS1corm/job_working_directory/000/4/RAxML_bestTree.galaxy - -Overall execution time: 0.917038 secs or 0.000255 hours or 0.000011 days - - -OM: CLI options DEBUG START: -<Values at 0x7f8e104919e0: {'bootseed': None, 'groupingfile': None, 'posterior_bootstopping_analysis': None, 'print_branch_lengths': None, 'starting_tree': None, 'model_opt_precision': None, 'weightfile': None, 'use_median_approximation': None, 'majority_rule_consensus': None, 'excludefile': None, 'save_memory_gappy_alignments': None, 'binary': 'raxmlHPC', 'numofcats': None, 'multistate_sub_model': None, 'multiple_model': None, 'search_complete_random_tree': None, 'source': '/tmp/tmpS1corm/files/000/dataset_7.dat', 'outgroup_name': None, 'estimate_individual_branch_lengths': None, 'ml_search_convergence': None, 'file_multiple_trees': None, 'rapid_bootstrap_random_seed': None, 'random_seed': 1234567890, 'disable_undetermined_seq_check': None, 'save_memory_cat_model': None, 'enable_evol_heuristics': None, 'aa_empirical_freq': None, 'threads': 1, 'external_protein_model': None, 'search_algorithm': 'd', 'constraint_file': None, 'secondary_structure_model': None, 'number_of_runs': 5, 'name': None, 'initial_rearrangement_setting': None, 'secondary_structure_file': None, 'model_type': 'nucleotide', 'aa_search_matrix': None, 'disable_rate_heterogeneity': None, 'base_model': 'GTRCAT', 'parsimony_starting_tree_only': None, 'number_of_runs_bootstop': None, 'sliding_window_size': None, 'bin_model_parameter_file': None}> -OM: CLI options DEBUG END +((Whale:0.00000100000050002909,(((Human:0.53594305845070155936,Seal:0.02530146292078635367):0.22193621954611089664,Frog:0.10286092072478680848):0.21862941933399418493,(Chicken:0.20757792196205043789,(Mouse:0.08330390883767016530,Rat:0.08037715347256141341):0.07528731153882931015):0.12712658591923928220):0.03338415401578518488):0.14391313040760642106,(Carp:0.35121248438619490084,Loach:0.00000100000050002909):0.21735437670664689569,Cow:0.06259549717909577982):0.0;