diff --git a/tools/raxml/raxml.py b/tools/raxml/raxml.py index 679526c21df..257e1b293c8 100644 --- a/tools/raxml/raxml.py +++ b/tools/raxml/raxml.py @@ -39,8 +39,6 @@ def __main__(): 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 @@ def __main__(): 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 @@ def __main__(): 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 @@ def __main__(): 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 @@ def __main__(): 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: diff --git a/tools/raxml/raxml.xml b/tools/raxml/raxml.xml index 8e775e5a893..ae6e6dc155f 100644 --- a/tools/raxml/raxml.xml +++ b/tools/raxml/raxml.xml @@ -1,7 +1,8 @@ - + - Maximum Likelihood based inference of large phylogenetic trees raxml + python 1 @@ -447,8 +448,8 @@ - - + + @@ -460,14 +461,13 @@ - + - - - + + diff --git a/tools/raxml/test-data/RAxML_parsimonyTree.galaxy.multi b/tools/raxml/test-data/RAxML_parsimonyTree.galaxy.multi index 4ea97615a4a..8efc1b56766 100644 --- a/tools/raxml/test-data/RAxML_parsimonyTree.galaxy.multi +++ b/tools/raxml/test-data/RAxML_parsimonyTree.galaxy.multi @@ -1,87 +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: - -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;