Mercurial > repos > iuc > raxml
annotate raxml.py @ 0:6805e85573b8 draft
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
author | iuc |
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date | Mon, 14 Nov 2016 14:03:39 -0500 |
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children | ba29b5e2a4be |
rev | line source |
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0
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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1 #!/usr/bin/env python |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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2 """ |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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3 Runs RAxML on a sequence file. |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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4 For use with RAxML version 8.2.4 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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5 """ |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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6 import fnmatch |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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7 import glob |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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8 import optparse |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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9 import os |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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10 import subprocess |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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11 import sys |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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12 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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13 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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14 def stop_err(msg): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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15 sys.stderr.write("%s\n" % msg) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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16 sys.exit() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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17 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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18 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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19 def getint(name): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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20 basename = name.partition('RUN.') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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21 if basename[2] != '': |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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22 num = basename[2] |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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23 return int(num) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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24 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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25 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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26 def __main__(): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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27 usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]" |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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28 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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29 # Parse the primary wrapper's command line options |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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30 parser = optparse.OptionParser(usage=usage) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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31 # raxml binary name, hardcoded in the xml file |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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32 parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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33 # (-a) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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34 parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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35 # (-A) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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36 parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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37 # (-b) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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38 parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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39 # (-c) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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40 parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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41 # (-d) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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42 parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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43 # (-D) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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44 parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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45 # (-e) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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46 parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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47 # (-E) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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48 parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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49 # (-f) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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50 parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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51 # (-F) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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52 parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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53 # (-g) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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54 parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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55 # (-G) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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56 parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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57 # (-i) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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58 parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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59 # (-I) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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60 parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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61 # (-J) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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62 parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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63 # (-k) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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64 parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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65 # (-K) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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66 parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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67 # (-m) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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68 parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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69 parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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70 parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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71 parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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72 # (-n) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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73 parser.add_option("--name", action="store", type="string", dest="name", help="Run Name") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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74 # (-N/#) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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75 parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", help="Number of alternative runs") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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76 parser.add_option("--number_of_runs_bootstop", action="store", type="string", dest="number_of_runs_bootstop", help="Number of alternative runs based on the bootstop criteria") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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77 # (-M) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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78 parser.add_option("--estimate_individual_branch_lengths", action="store_true", dest="estimate_individual_branch_lengths", help="Estimate individual branch lengths") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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79 # (-o) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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80 parser.add_option("--outgroup_name", action="store", type="string", dest="outgroup_name", help="Outgroup Name") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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81 # (-O) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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82 parser.add_option("--disable_undetermined_seq_check", action="store_true", dest="disable_undetermined_seq_check", help="Disable undetermined sequence check") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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83 # (-p) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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84 parser.add_option("--random_seed", action="store", type="int", dest="random_seed", help="Random Number Seed") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
85 # (-P) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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86 parser.add_option("--external_protein_model", action="store", type="string", dest="external_protein_model", help="External Protein Model") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
87 # (-q) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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88 parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
89 # (-r) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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90 parser.add_option("--constraint_file", action="store", type="string", dest="constraint_file", help="Constraint File") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
91 # (-R) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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92 parser.add_option("--bin_model_parameter_file", action="store", type="string", dest="bin_model_parameter_file", help="Constraint File") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
93 # (-s) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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94 parser.add_option("--source", action="store", type="string", dest="source", help="Input file") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
95 # (-S) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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96 parser.add_option("--secondary_structure_file", action="store", type="string", dest="secondary_structure_file", help="Secondary structure file") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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changeset
|
97 # (-t) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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98 parser.add_option("--starting_tree", action="store", type="string", dest="starting_tree", help="Starting Tree") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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99 # (-T) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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100 parser.add_option("--threads", action="store", type="int", dest="threads", help="Number of threads to use") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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101 # (-u) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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102 parser.add_option("--use_median_approximation", action="store_true", dest="use_median_approximation", help="Use median approximation") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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103 # (-U) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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104 parser.add_option("--save_memory_gappy_alignments", action="store_true", dest="save_memory_gappy_alignments", help="Save memory in large gapped alignments") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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105 # (-V) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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106 parser.add_option("--disable_rate_heterogeneity", action="store_true", dest="disable_rate_heterogeneity", help="Disable rate heterogeneity") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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107 # (-W) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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108 parser.add_option("--sliding_window_size", action="store", type="string", dest="sliding_window_size", help="Sliding window size") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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109 # (-x) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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110 parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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111 # (-y) |
6805e85573b8
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112 parser.add_option("--parsimony_starting_tree_only", action="store_true", dest="parsimony_starting_tree_only", help="Generate a parsimony starting tree only") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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113 # (-z) |
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114 parser.add_option("--file_multiple_trees", action="store", type="string", dest="file_multiple_trees", help="Multiple Trees File") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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115 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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116 (options, args) = parser.parse_args() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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117 cmd = [] |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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118 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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119 # Required parameters |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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120 binary = options.binary |
6805e85573b8
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121 cmd.append(binary) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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122 # Threads |
6805e85573b8
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123 if options.threads > 1: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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124 threads = "-T %d" % options.threads |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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125 cmd.append(threads) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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126 # Source |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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127 source = "-s %s" % options.source |
6805e85573b8
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128 cmd.append(source) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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129 # Hardcode to "galaxy" first to simplify the output part of the wrapper |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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130 # name = "-n %s" % options.name |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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131 name = "-n galaxy" |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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132 cmd.append(name) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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133 # Model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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134 model_type = options.model_type |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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135 base_model = options.base_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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136 aa_search_matrix = options.aa_search_matrix |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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137 aa_empirical_freq = options.aa_empirical_freq |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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138 if model_type == 'aminoacid': |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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139 model = "-m %s%s" % (base_model, aa_search_matrix) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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140 if aa_empirical_freq: |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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141 model = "-m %s%s%s" % (base_model, aa_search_matrix, 'F') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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142 # (-P) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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143 if options.external_protein_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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144 external_protein_model = "-P %s" % options.external_protein_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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145 cmd.append(external_protein_model) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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146 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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147 model = "-m %s" % base_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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148 cmd.append(model) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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149 if model == "GTRCAT": |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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150 # (-c) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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151 if options.numofcats: |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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152 numofcats = "-c %d" % options.numofcats |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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153 cmd.append(numofcats) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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154 # Optional parameters |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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155 if options.number_of_runs_bootstop: |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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156 number_of_runs_bootstop = "-N %s" % options.number_of_runs_bootstop |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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157 cmd.append(number_of_runs_bootstop) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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158 else: |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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159 number_of_runs_bootstop = '' |
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160 if options.number_of_runs: |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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161 number_of_runs_opt = "-N %d" % options.number_of_runs |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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162 cmd.append(number_of_runs_opt) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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163 else: |
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164 number_of_runs_opt = 0 |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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165 # (-a) |
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166 if options.weightfile: |
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167 weightfile = "-a %s" % options.weightfile |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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168 cmd.append(weightfile) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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169 # (-A) |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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170 if options.secondary_structure_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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171 secondary_structure_model = "-A %s" % options.secondary_structure_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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172 cmd.append(secondary_structure_model ) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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173 # (-b) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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174 if options.bootseed: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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175 bootseed = "-b %d" % options.bootseed |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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176 cmd.append(bootseed) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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177 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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178 bootseed = 0 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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179 # -C - doesn't work in pthreads version, skipped |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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180 if options.search_complete_random_tree: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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181 cmd.append("-d") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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182 if options.ml_search_convergence: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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183 cmd.append("-D" ) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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184 if options.model_opt_precision: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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185 model_opt_precision = "-e %f" % options.model_opt_precision |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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186 cmd.append(model_opt_precision) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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187 if options.excludefile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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188 excludefile = "-E %s" % options.excludefile |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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189 cmd.append(excludefile) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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190 if options.search_algorithm: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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191 search_algorithm = "-f %s" % options.search_algorithm |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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192 cmd.append(search_algorithm) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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193 if options.save_memory_cat_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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194 cmd.append("-F") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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195 if options.groupingfile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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196 groupingfile = "-g %s" % options.groupingfile |
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planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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197 cmd.append(groupingfile) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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198 if options.enable_evol_heuristics: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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199 enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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200 cmd.append(enable_evol_heuristics ) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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201 if options.initial_rearrangement_setting: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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202 initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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203 cmd.append(initial_rearrangement_setting) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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204 if options.posterior_bootstopping_analysis: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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205 posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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206 cmd.append(posterior_bootstopping_analysis) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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207 if options.majority_rule_consensus: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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208 majority_rule_consensus = "-J %s" % options.majority_rule_consensus |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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209 cmd.append(majority_rule_consensus) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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210 if options.print_branch_lengths: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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211 cmd.append("-k") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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212 if options.multistate_sub_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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213 multistate_sub_model = "-K %s" % options.multistate_sub_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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214 cmd.append(multistate_sub_model) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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215 if options.estimate_individual_branch_lengths: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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216 cmd.append("-M") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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217 if options.outgroup_name: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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218 outgroup_name = "-o %s" % options.outgroup_name |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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219 cmd.append(outgroup_name) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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220 if options.disable_undetermined_seq_check: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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221 cmd.append("-O") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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|
222 if options.random_seed: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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223 random_seed = "-p %d" % options.random_seed |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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|
224 cmd.append(random_seed) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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225 multiple_model = None |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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226 if options.multiple_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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227 multiple_model = "-q %s" % options.multiple_model |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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228 cmd.append(multiple_model) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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229 if options.constraint_file: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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230 constraint_file = "-r %s" % options.constraint_file |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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231 cmd.append(constraint_file) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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232 if options.bin_model_parameter_file: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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233 bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy" |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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234 os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name ) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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235 bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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236 # Needs testing. Is the hardcoded name or the real path needed? |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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237 cmd.append(bin_model_parameter_file) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
238 if options.secondary_structure_file: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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239 secondary_structure_file = "-S %s" % options.secondary_structure_file |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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240 cmd.append(secondary_structure_file) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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changeset
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241 if options.starting_tree: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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242 starting_tree = "-t %s" % options.starting_tree |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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243 cmd.append(starting_tree) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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244 if options.use_median_approximation: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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245 cmd.append("-u") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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246 if options.save_memory_gappy_alignments: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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247 cmd.append("-U") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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248 if options.disable_rate_heterogeneity: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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249 cmd.append("-V") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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250 if options.sliding_window_size: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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251 sliding_window_size = "-W %d" % options.sliding_window_size |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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252 cmd.append(sliding_window_size) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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253 if options.rapid_bootstrap_random_seed: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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254 rapid_bootstrap_random_seed = "-x %d" % options.rapid_bootstrap_random_seed |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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255 cmd.append(rapid_bootstrap_random_seed) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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changeset
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256 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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257 rapid_bootstrap_random_seed = 0 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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changeset
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258 if options.parsimony_starting_tree_only: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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259 cmd.append("-y") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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260 if options.file_multiple_trees: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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|
261 file_multiple_trees = "-z %s" % options.file_multiple_trees |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
262 cmd.append(file_multiple_trees) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
263 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
264 print "cmd list: ", cmd, "\n" |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
265 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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266 full_cmd = " ".join(cmd) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
267 print "Command string: %s" % full_cmd |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
268 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
269 try: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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diff
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270 proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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271 except Exception as err: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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272 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err)) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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273 sys.exit(1) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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|
274 stdout, stderr = proc.communicate() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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275 return_code = proc.returncode |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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changeset
|
276 if return_code: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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277 sys.stdout.write(stdout) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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278 sys.stderr.write(stderr) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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279 sys.stderr.write("Return error code %i from command:\n" % return_code) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
|
280 sys.stderr.write("%s\n" % cmd) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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281 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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282 sys.stdout.write(stdout) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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283 sys.stdout.write(stderr) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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|
284 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
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285 # Multiple runs - concatenate |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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286 if number_of_runs_opt > 0: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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|
287 if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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288 runfiles = glob.glob('RAxML*RUN*') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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289 runfiles.sort(key=getint) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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changeset
|
290 # Logs |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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291 outfile = open('RAxML_log.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
|
292 for filename in runfiles: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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293 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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|
294 infile = open(filename, 'r') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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295 filename_line = "%s\n" % filename |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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296 outfile.write(filename_line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
297 for line in infile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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298 outfile.write(line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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299 infile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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|
300 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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changeset
|
301 # Parsimony Trees |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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302 outfile = open('RAxML_parsimonyTree.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
|
303 for filename in runfiles: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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304 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
305 infile = open(filename, 'r') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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306 filename_line = "%s\n" % filename |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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diff
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|
307 outfile.write(filename_line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
|
308 for line in infile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
309 outfile.write(line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
310 infile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
311 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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changeset
|
312 # Results |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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313 outfile = open('RAxML_result.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
314 for filename in runfiles: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
315 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
316 infile = open(filename, 'r') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
changeset
|
317 filename_line = "%s\n" % filename |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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318 outfile.write(filename_line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
319 for line in infile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
320 outfile.write(line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
321 infile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
322 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
323 # Multiple Model Partition Files |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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|
324 if multiple_model: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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325 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
326 if len(files) > 0: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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327 files.sort(key=getint) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff
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|
328 outfile = open('RAxML_bestTreePartitions.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
329 # Best Tree Partitions |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
330 for filename in files: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
331 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
332 infile = open(filename, 'r') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
333 filename_line = "%s\n" % filename |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
334 outfile.write(filename_line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
335 for line in infile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
336 outfile.write(line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
337 infile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
338 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
339 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
340 outfile = open('RAxML_bestTreePartitions.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
341 outfile.write("No partition files were produced.\n") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
342 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
343 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
344 # Result Partitions |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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|
345 files = glob.glob('RAxML_result.galaxy.PARTITION.*') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
346 if len(files) > 0: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
347 files.sort(key=getint) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
348 outfile = open('RAxML_resultPartitions.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
349 for filename in files: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
350 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
351 infile = open(filename, 'r') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
352 filename_line = "%s\n" % filename |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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353 outfile.write(filename_line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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354 for line in infile: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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355 outfile.write(line) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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356 infile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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357 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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358 else: |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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359 outfile = open('RAxML_resultPartitions.galaxy', 'w') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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360 outfile.write("No partition files were produced.\n") |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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361 outfile.close() |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
362 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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363 # DEBUG options |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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364 infof = open('RAxML_info.galaxy', 'a') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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365 infof.write('\nOM: CLI options DEBUG START:\n') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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366 infof.write(options.__repr__()) |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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367 infof.write('\nOM: CLI options DEBUG END\n') |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
|
368 |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
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369 if __name__ == "__main__": |
6805e85573b8
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff
changeset
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370 __main__() |