| Next changeset 1:ba29b5e2a4be (2017-06-27) |
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Commit message:
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f |
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added:
acknowledgement.md raxml.py raxml.xml test-data/RAxML_parsimonyTree.galaxy.basic test-data/RAxML_parsimonyTree.galaxy.multi test-data/dna.fasta test-data/dna.phy tool_dependencies.xml |
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| diff -r 000000000000 -r 6805e85573b8 acknowledgement.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/acknowledgement.md Mon Nov 14 14:03:39 2016 -0500 |
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| @@ -0,0 +1,10 @@ +RAxML for Galaxy +================ + +95% of this work was made by Oleksandr Moskalenko. Tiago Antao +is trying to update it to a more current version. + +Acknowledgements +---------------- + +Björn Grüning for all the help |
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| diff -r 000000000000 -r 6805e85573b8 raxml.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raxml.py Mon Nov 14 14:03:39 2016 -0500 |
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| b'@@ -0,0 +1,370 @@\n+#!/usr/bin/env python\n+"""\n+Runs RAxML on a sequence file.\n+For use with RAxML version 8.2.4\n+"""\n+import fnmatch\n+import glob\n+import optparse\n+import os\n+import subprocess\n+import sys\n+\n+\n+def stop_err(msg):\n+ sys.stderr.write("%s\\n" % msg)\n+ sys.exit()\n+\n+\n+def getint(name):\n+ basename = name.partition(\'RUN.\')\n+ if basename[2] != \'\':\n+ num = basename[2]\n+ return int(num)\n+\n+\n+def __main__():\n+ usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]"\n+\n+ # Parse the primary wrapper\'s command line options\n+ parser = optparse.OptionParser(usage=usage)\n+ # raxml binary name, hardcoded in the xml file\n+ parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run")\n+ # (-a)\n+ parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file")\n+ # (-A)\n+ parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model")\n+ # (-b)\n+ parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed")\n+ # (-c)\n+ parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories")\n+ # (-d)\n+ parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree")\n+ # (-D)\n+ parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion")\n+ # (-e)\n+ parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)")\n+ # (-E)\n+ parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name")\n+ # (-f)\n+ parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm")\n+ # (-F)\n+ parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models")\n+ # (-g)\n+ parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name")\n+ # (-G)\n+ parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics")\n+ # (-i)\n+ parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting")\n+ # (-I)\n+ parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis")\n+ # (-J)\n+ parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus")\n+ # (-k)\n+ parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths")\n+ # (-K)\n+ parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model")\n+ # (-m)\n+ parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type")\n+ parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model")\n+ parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences")\n+ parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix")\n+ # (-n)\n+ parser.add_option("--name", action="store", type="string", dest="name", help="Run Name")\n+ # (-N/#)\n+ pars'..b'returncode\n+ if return_code:\n+ sys.stdout.write(stdout)\n+ sys.stderr.write(stderr)\n+ sys.stderr.write("Return error code %i from command:\\n" % return_code)\n+ sys.stderr.write("%s\\n" % cmd)\n+ else:\n+ sys.stdout.write(stdout)\n+ sys.stdout.write(stderr)\n+\n+ # Multiple runs - concatenate\n+ if number_of_runs_opt > 0:\n+ if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ):\n+ runfiles = glob.glob(\'RAxML*RUN*\')\n+ runfiles.sort(key=getint)\n+ # Logs\n+ outfile = open(\'RAxML_log.galaxy\', \'w\')\n+ for filename in runfiles:\n+ if fnmatch.fnmatch(filename, \'RAxML_log.galaxy.RUN.*\'):\n+ infile = open(filename, \'r\')\n+ filename_line = "%s\\n" % filename\n+ outfile.write(filename_line)\n+ for line in infile:\n+ outfile.write(line)\n+ infile.close()\n+ outfile.close()\n+ # Parsimony Trees\n+ outfile = open(\'RAxML_parsimonyTree.galaxy\', \'w\')\n+ for filename in runfiles:\n+ if fnmatch.fnmatch(filename, \'RAxML_parsimonyTree.galaxy.RUN.*\'):\n+ infile = open(filename, \'r\')\n+ filename_line = "%s\\n" % filename\n+ outfile.write(filename_line)\n+ for line in infile:\n+ outfile.write(line)\n+ infile.close()\n+ outfile.close()\n+ # Results\n+ outfile = open(\'RAxML_result.galaxy\', \'w\')\n+ for filename in runfiles:\n+ if fnmatch.fnmatch(filename, \'RAxML_result.galaxy.RUN.*\'):\n+ infile = open(filename, \'r\')\n+ filename_line = "%s\\n" % filename\n+ outfile.write(filename_line)\n+ for line in infile:\n+ outfile.write(line)\n+ infile.close()\n+ outfile.close()\n+ # Multiple Model Partition Files\n+ if multiple_model:\n+ files = glob.glob(\'RAxML_bestTree.galaxy.PARTITION.*\')\n+ if len(files) > 0:\n+ files.sort(key=getint)\n+ outfile = open(\'RAxML_bestTreePartitions.galaxy\', \'w\')\n+ # Best Tree Partitions\n+ for filename in files:\n+ if fnmatch.fnmatch(filename, \'RAxML_bestTree.galaxy.PARTITION.*\'):\n+ infile = open(filename, \'r\')\n+ filename_line = "%s\\n" % filename\n+ outfile.write(filename_line)\n+ for line in infile:\n+ outfile.write(line)\n+ infile.close()\n+ outfile.close()\n+ else:\n+ outfile = open(\'RAxML_bestTreePartitions.galaxy\', \'w\')\n+ outfile.write("No partition files were produced.\\n")\n+ outfile.close()\n+\n+ # Result Partitions\n+ files = glob.glob(\'RAxML_result.galaxy.PARTITION.*\')\n+ if len(files) > 0:\n+ files.sort(key=getint)\n+ outfile = open(\'RAxML_resultPartitions.galaxy\', \'w\')\n+ for filename in files:\n+ if fnmatch.fnmatch(filename, \'RAxML_result.galaxy.PARTITION.*\'):\n+ infile = open(filename, \'r\')\n+ filename_line = "%s\\n" % filename\n+ outfile.write(filename_line)\n+ for line in infile:\n+ outfile.write(line)\n+ infile.close()\n+ outfile.close()\n+ else:\n+ outfile = open(\'RAxML_resultPartitions.galaxy\', \'w\')\n+ outfile.write("No partition files were produced.\\n")\n+ outfile.close()\n+\n+ # DEBUG options\n+ infof = open(\'RAxML_info.galaxy\', \'a\')\n+ infof.write(\'\\nOM: CLI options DEBUG START:\\n\')\n+ infof.write(options.__repr__())\n+ infof.write(\'\\nOM: CLI options DEBUG END\\n\')\n+\n+if __name__ == "__main__":\n+ __main__()\n' |
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| diff -r 000000000000 -r 6805e85573b8 raxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raxml.xml Mon Nov 14 14:03:39 2016 -0500 |
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| b'@@ -0,0 +1,545 @@\n+<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2">\n+ <description>- Maximum Likelihood based inference of large phylogenetic trees</description>\n+ <requirements>\n+ <requirement type=\'package\' version="8.2.4">raxml</requirement>\n+ </requirements>\n+ <command interpreter="python">raxml.py\n+ ## Required parameters \n+ ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1\n+ ## (-T)\n+ ## Cannot have --threads 1\n+ #set $slots = $getVar(\'GALAXY_SLOTS\', 1)\n+ #if $slots == 1:\n+ --binary "raxmlHPC"\n+ --threads 1\n+ #else:\n+ --binary "raxmlHPC-PTHREADS"\n+ --threads $slots\n+ #end if\n+ ## (-s)\n+ --source "$infile"\n+ ## (-m)\n+ --model_type $search_model_selector.model_type\n+ --base_model $search_model_selector.base_model\n+ #if str( $search_model_selector.model_type ) == \'aminoacid\':\n+ $search_model_selector.aa_model_empirical_base_frequencies\n+ #if $search_model_selector.aa_search_matrix:\n+ --aa_search_matrix $search_model_selector.aa_search_matrix\n+ #end if\n+ #end if\n+\n+ ## Optional parameters\n+\n+ #if str( $selExtraOpts.extraOptions ) == \'full\':\n+ ## (-N/#)\n+ #if $selExtraOpts.number_of_runs:\n+ --number_of_runs $selExtraOpts.number_of_runs\n+ #end if\n+ #if $selExtraOpts.number_of_runs_bootstop:\n+ --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop\n+ #end if\n+ ## (-a)\n+ #if $selExtraOpts.weightfile:\n+ --weightfile "$selExtraOpts.weightfile"\n+ #end if\n+ ## (-b)\n+ #if str ($selExtraOpts.secondary_structure_model) != "":\n+ --secondary_structure_model $selExtraOpts.secondary_structure_model\n+ #end if\n+ ## (-b)\n+ #if str($selExtraOpts.bootseed):\n+ --bootseed $selExtraOpts.bootseed\n+ #end if\n+ ## (-c)\n+ #if $selExtraOpts.numofcats:\n+ --numofcats $selExtraOpts.numofcats\n+ #end if\n+ ## (-d)\n+ $selExtraOpts.search_complete_random_tree\n+ ## (-D)\n+ $selExtraOpts.ml_search_convergence\n+ ## (-e)\n+ #if $selExtraOpts.model_opt_precision:\n+ --model_opt_precision $selExtraOpts.model_opt_precision\n+ #end if\n+ ## (-E)\n+ #if $selExtraOpts.excludefile:\n+ --excludefile "$selExtraOpts.excludefile"\n+ #end if\n+ ## (-f)\n+ #if $selExtraOpts.search_algorithm:\n+ --search_algorithm $selExtraOpts.search_algorithm\n+ #end if\n+ ## (-F)\n+ $selExtraOpts.save_memory_cat_model\n+ ## (-g)\n+ #if $selExtraOpts.groupingfile:\n+ --groupingfile "$selExtraOpts.groupingfile"\n+ #end if\n+ ## (-G)\n+ #if $selExtraOpts.enable_evol_heuristics:\n+ --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics\n+ #end if\n+ ## (-i)\n+ #if $selExtraOpts.initial_rearrangement_setting:\n+ --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting\n+ #end if\n+ ## (-I)\n+ #if $selExtraOpts.posterior_bootstopping_analysis:\n+ --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis\n+ #end if\n+ ## (-J)\n+ #if $selExtraOpts.majority_rule_consensus:\n+ --majority_rule_consensus $selExtraOpts.majority_rule_consensus\n+ #end if\n+ ## (-k)\n+ $selExtraOpts.print_branch_lengths\n+ ## (-K)\n+ #if str ($selExtraOpts.multistate_sub_model) != "":\n+ --multistate_sub_model $selExtraOpts.multistate_sub_model\n+ #end if\n+ ## (-m) - see elsewhere\n+ ## (-M)\n+ $selExtraOpts.estimate_individual_branch_lengths\n+ ## (-n) - see elsewhere\n+ ## (-o)\n+ #if $selExtraOpts.outgroup_name:\n+ --outgroup_name "$selExtraOpts.outgrou'..b'gorithm\'] == \'b\') or ((selExtraOpts[\'search_algorithm\'] == \'a\') and (selExtraOpts[\'rapid_bootstrap_random_seed\'] != \'\')) </filter>\n+ </data>\n+ <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ <filter>(selExtraOpts[\'majority_rule_consensus\'] == \'STRICT\') </filter>\n+ </data>\n+ <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ <filter>(selExtraOpts[\'majority_rule_consensus\'] == \'MR\')</filter>\n+ </data>\n+ <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ <filter>(selExtraOpts[\'majority_rule_consensus\'] == \'MRE\')</filter>\n+ </data>\n+ <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">\n+ <filter>selExtraOpts[\'search_algorithm\'] == \'m\' </filter>\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ </data>\n+ <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">\n+ <filter>selExtraOpts[\'search_algorithm\'] == \'g\' </filter>\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ </data>\n+ <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">\n+ <filter>selExtraOpts[\'search_algorithm\'] == \'x\' </filter>\n+ <filter>selExtraOpts[\'extraOptions\'] == "full"</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="extraOptions" value="required"/>\n+ <param name="infile" value="dna.phy"/>\n+ <param name="model_type" value="nucleotide"/>\n+ <param name="base_model" value="GTRCAT"/>\n+ <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" />\n+ <output name="bestTree">\n+ <assert_contents>\n+ <has_text_matching expression="Frog" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="extraOptions" value="full"/>\n+ <param name="infile" value="dna.fasta"/>\n+ <param name="model_type" value="nucleotide"/>\n+ <param name="base_model" value="GTRCAT"/>\n+ <param name="number_of_runs" value="5"/>\n+ <output name="parsimonyTree">\n+ <assert_contents>\n+ <has_text_matching expression="Chicken" />\n+ <has_text_matching expression="RUN.4" />\n+ </assert_contents>\n+ </output>\n+ <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/>\n+ <output name="bestTree">\n+ <assert_contents>\n+ <has_text_matching expression="Whale" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+\n+RAxML_ (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic\n+trees. The program is explicitly being developed to efficiently infer trees for\n+extremely large datasets, either in terms of the number of taxa and/or the\n+sequence length.\n+\n+\n+.. _RAxML: http://www.exelixis-lab.org/\n+\n+\n+**Tool development**:\n+\n+Oleksandr Moskalenko with adaptations from Tiago Antao.\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu033</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 6805e85573b8 test-data/RAxML_parsimonyTree.galaxy.basic --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_parsimonyTree.galaxy.basic Mon Nov 14 14:03:39 2016 -0500 |
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| @@ -0,0 +1,1 @@ +(Whale,((((Mouse,Chicken),Human),Rat),((Frog,(Carp,Loach)),Seal)),Cow); |
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| diff -r 000000000000 -r 6805e85573b8 test-data/RAxML_parsimonyTree.galaxy.multi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_parsimonyTree.galaxy.multi Mon Nov 14 14:03:39 2016 -0500 |
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| @@ -0,0 +1,87 @@ + + +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 |
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| diff -r 000000000000 -r 6805e85573b8 test-data/dna.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna.fasta Mon Nov 14 14:03:39 2016 -0500 |
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| @@ -0,0 +1,20 @@ +>Cow +ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA +>Carp +ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT +>Chicken +ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC +>Human +ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT +>Loach +ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT +>Mouse +ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA +>Rat +ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT +>Seal +ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA +>Whale +ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC +>Frog +ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA |
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| diff -r 000000000000 -r 6805e85573b8 test-data/dna.phy --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna.phy Mon Nov 14 14:03:39 2016 -0500 |
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| @@ -0,0 +1,11 @@ +10 60 +Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA +Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT +Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC +Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT +Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT +Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA +Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT +Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA +Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC +Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA \ No newline at end of file |
| b |
| diff -r 000000000000 -r 6805e85573b8 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 14 14:03:39 2016 -0500 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="raxml" version="8.2.4"> + <repository changeset_revision="34be595fd2a9" name="package_raxml_8_2_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |