# HG changeset patch
# User iuc
# Date 1575291130 18000
# Node ID a4b71be30c3c8e12208de300ba800cc39fa35c24
# Parent  ba29b5e2a4be345857a03bd97bcded286b1ad7ed
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"

diff -r ba29b5e2a4be -r a4b71be30c3c raxml.py
--- 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:
diff -r ba29b5e2a4be -r a4b71be30c3c raxml.xml
--- 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>
diff -r ba29b5e2a4be -r a4b71be30c3c test-data/RAxML_parsimonyTree.galaxy.multi
--- 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;