{"action":"created","comment":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/45765953","id":45765953,"diff_hunk":"@@ -0,0 +1,593 @@\n+<tool id=\"raxml\" name=\"Phyogenetic reconstruction with RaXML\" version=\"1.0.1\">\n+  <description>- Maximum Likelihood based inference of large phylogenetic trees</description>\n+  <requirements>\n+    <requirement type='package' version=\"8.2.4\">raxml</requirement>\n+  </requirements>\n+  <command interpreter=\"python\">raxml.py\n+    ## Required parameters \n+    ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1\n+    ## (-T)\n+    ## Cannot have --threads 1\n+    #set $slots = $getVar('GALAXY_SLOTS', 1)\n+    #if $slots == 1:\n+        --binary \"raxmlHPC\"\n+        --threads 1\n+    #else:\n+        --binary \"raxmlHPC-PTHREADS\"\n+        --threads $slots\n+    #end if\n+    ## (-s)\n+    --source $infile\n+    ## (-m)\n+    --model_type $search_model_selector.model_type\n+    --base_model $search_model_selector.base_model\n+    #if str( $search_model_selector.model_type ) == 'aminoacid':\n+        $search_model_selector.aa_model_empirical_base_frequencies\n+        #if $search_model_selector.aa_search_matrix:\n+            --aa_search_matrix $search_model_selector.aa_search_matrix\n+        #end if\n+    #end if\n+    ## (-p)\n+    #if $random_seed:\n+        --random_seed $random_seed\n+    #else\n+        --random_seed 1234567890\n+    #end if\n+\n+    ## Optional parameters\n+\n+#if str( $selExtraOpts.extraOptions ) == 'full':\n+    ## (-N/#)\n+    #if $selExtraOpts.number_of_runs:\n+        --number_of_runs $selExtraOpts.number_of_runs\n+    #end if\n+    #if $selExtraOpts.number_of_runs_bootstop:\n+        --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop\n+    #end if\n+    ## (-a)\n+    #if $selExtraOpts.weightfile:\n+        --weightfile $selExtraOpts.weightfile\n+    #end if\n+    ## (-b)\n+    #if str ($selExtraOpts.secondary_structure_model) != \"\":\n+        --secondary_structure_model $selExtraOpts.secondary_structure_model\n+    #end if\n+    ## (-b)\n+    #if $selExtraOpts.bootseed:\n+        --bootseed $selExtraOpts.bootseed\n+    #end if\n+    ## (-c)\n+    #if $selExtraOpts.numofcats:\n+        --numofcats $selExtraOpts.numofcats\n+    #end if\n+    ## (-d)\n+    $selExtraOpts.search_complete_random_tree\n+    ## (-D)\n+    $selExtraOpts.ml_search_convergence\n+    ## (-e)\n+    #if $selExtraOpts.model_opt_precision:\n+        --model_opt_precision $selExtraOpts.model_opt_precision\n+    #end if\n+    ## (-E)\n+    #if $selExtraOpts.excludefile:\n+        --excludefile $selExtraOpts.excludefile\n+    #end if\n+    ## (-f)\n+    #if $selExtraOpts.search_algorithm:\n+        --search_algorithm $selExtraOpts.search_algorithm\n+    #end if\n+    ## (-F)\n+    $selExtraOpts.save_memory_cat_model\n+    ## (-g)\n+    #if $selExtraOpts.groupingfile:\n+        --groupingfile $selExtraOpts.groupingfile\n+    #end if\n+    ## (-G)\n+    #if $selExtraOpts.enable_evol_heuristics:\n+        --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics\n+    #end if\n+    ## (-i)\n+    #if $selExtraOpts.initial_rearrangement_setting:\n+        --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting\n+    #end if\n+    ## (-I)\n+    #if $selExtraOpts.posterior_bootstopping_analysis:\n+        --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis\n+    #end if\n+    ## (-J)\n+    #if $selExtraOpts.majority_rule_consensus:\n+        --majority_rule_consensus $selExtraOpts.majority_rule_consensus\n+    #end if\n+    ## (-k)\n+    $selExtraOpts.print_branch_lengths\n+    ## (-K)\n+    #if str ($selExtraOpts.multistate_sub_model) != \"\":\n+        --multistate_sub_model $selExtraOpts.multistate_sub_model\n+    #end if\n+    ## (-m) - see elsewhere\n+    ## (-M)\n+    $selExtraOpts.estimate_individual_branch_lengths\n+    ## (-n) - see elsewhere\n+    ## (-o)\n+    #if $selExtraOpts.outgroup_name:\n+        --outgroup_name $selExtraOpts.outgroup_name\n+    #end if\n+    ## (-O)\n+    $selExtraOpts.disable_undetermined_seq_check\n+    ## (-P)\n+    #if $selExtraOpts.external_protein_model:\n+        --external_protein_model $selExtraOpts.external_protein_model\n+    #end if\n+    ## (-q)\n+    #if $selExtraOpts.multiple_model:\n+        --multiple_model $selExtraOpts.multiple_model\n+    #end if\n+    ## (-r)\n+    #if $selExtraOpts.constraint_file:\n+        --constraint_file $selExtraOpts.constraint_file\n+    #end if\n+    ## (-R)\n+    #if $selExtraOpts.bin_model_parameter_file:\n+        --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file\n+    #end if\n+    ## (-S)\n+    #if $selExtraOpts.secondary_structure_file:\n+        --secondary_structure_file $selExtraOpts.secondary_structure_file\n+    #end if\n+    ## (-t)\n+    #if $selExtraOpts.start_tree_file:\n+        --starting_tree $selExtraOpts.start_tree_file\n+    #end if\n+    ## (-T) see elsewhere\n+    ## (-u)\n+    $selExtraOpts.use_median_approximation\n+    ## (-U)\n+    $selExtraOpts.save_memory_gappy_alignments\n+    ## (-V)\n+    $selExtraOpts.disable_rate_heterogeneity\n+    ## (-W)\n+    #if $selExtraOpts.sliding_window_size:\n+        --sliding_window_size $selExtraOpts.sliding_window_size\n+    #end if\n+    ## (-x)\n+    #if $selExtraOpts.rapid_bootstrap_random_seed:\n+        --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed\n+    #end if\n+    ## (-y)\n+    $selExtraOpts.parsimony_starting_tree_only\n+    ## (-z)\n+    #if $selExtraOpts.file_multiple_trees:\n+        --file_multiple_trees $selExtraOpts.file_multiple_trees\n+    #end if\n+#end if\n+\n+    </command>\n+  <inputs>\n+    ## (-s)\n+    <param type=\"data\" format=\"fasta,phylip\" name=\"infile\" label=\"Source file\" help=\"(-s)\"/> \n+    ## (-m)\n+    <conditional name=\"search_model_selector\">\n+        <param name=\"model_type\" type=\"select\" label=\"Model Type\" help=\"(--model_type)\">\n+            <option value=\"nucleotide\" selected=\"true\">Nucleotide</option>\n+            <option value=\"aminoacid\">Amino Acid</option>\n+            <option value=\"binary\">Binary</option>\n+            <option value=\"multistate\">Multistate</option>\n+        </param>\n+        <when value=\"nucleotide\">\n+    ## Nucleotide substitution models\n+            <param name=\"base_model\" type=\"select\" label=\"Substitution Model\" help=\"--base-model\">\n+                <option value=\"GTRCAT\">GTRCAT</option> \n+                <option value=\"GTRCATI\">GTRCATI</option> \n+                <option value=\"GTRGAMMA\" select=\"true\">GTRGAMMA</option>\n+                <option value=\"GTRGAMMAI\">GTRGAMMAI</option>\n+            </param>\n+        </when>\n+    ## Aminoacid substitution models\n+        <when value=\"aminoacid\">\n+            <param name=\"aa_model_empirical_base_frequencies\"\n+                type=\"boolean\" checked=\"no\" truevalue=\"--aa_empirical_freq\" falsevalue=\"\" display=\"checkboxes\" label=\"Use empirical base frequencies in AA models\" />\n+            <param name=\"base_model\" type=\"select\" label=\"Substitution Model (--base_model)\">\n+                <option value=\"PROTCAT\" select=\"true\">PROTCAT</option>\n+                <option value=\"PROTCATI\">PROTCATI</option>\n+                <option value=\"PROTGAMMA\">PROTGAMMA</option>\n+                <option value=\"PROTGAMMAI\">PROTGAMMAI</option>\n+            </param>\n+            <param name=\"aa_search_matrix\" type=\"select\" label=\"Matrix\" help=\"(--aa_search_matrix)\">\n+                <option value=\"DAYHOFF\" select=\"true\">DAYHOFF</option>\n+                <option value=\"DCMUT\">DCMUT</option>\n+                <option value=\"JTT\">JTT</option>\n+                <option value=\"MTREV\">MTREV</option>\n+                <option value=\"WAG\">WAG</option>\n+                <option value=\"RTREV\">RTREV</option>\n+                <option value=\"CPREV\">CPREV</option>\n+                <option value=\"VT\">VT</option>\n+                <option value=\"BLOSUM62\">BLOSUM62</option>\n+                <option value=\"MTMAM\">MTMAM</option>\n+                <option value=\"LG\">LG</option>\n+                <option value=\"MTART\">MTART</option>\n+                <option value=\"MTZOA\">MTZOA</option>\n+                <option value=\"PMB\">PMB</option>\n+                <option value=\"HIVB\">HIVB</option>\n+                <option value=\"HIVW\">HIVW</option>\n+                <option value=\"JTTDCMUT\">JTTDCMUT</option>\n+                <option value=\"FLU\">FLU</option>\n+                <option value=\"DUMMY\">DUMMY</option>\n+                <option value=\"DUMMY2\">DUMMY2</option>\n+                <option value=\"GTR_UNLINKED\">GTR_UNLINKED</option>\n+                <option value=\"GTR\">GTR</option>\n+            </param>\n+        </when>\n+## Binary substitution models\n+        <when value=\"binary\">\n+            <param name=\"base_model\" type=\"select\" label=\"Substitution Model\" help=\"(--base_model)\">\n+                <option value=\"BINCAT\">BINCAT</option> \n+                <option value=\"BINCATI\">BINCATI</option> \n+                <option value=\"BINGAMMA\">BINGAMMA</option> \n+                <option value=\"BINGAMMAI\">BINGAMMAI</option> \n+            </param>\n+        </when>\n+## Multi-state substitution models\n+        <when value=\"multistate\">\n+            <param name=\"base_model\" type=\"select\" label=\"Substitution Model\">\n+                <option value=\"MULTICAT\">MULTICAT</option> \n+                <option value=\"MULTICATI\">MULTICATI</option> \n+                <option value=\"MULTIGAMMA\">MULTIGAMMA</option> \n+                <option value=\"MULTIGAMMAI\">MULTIGAMMAI</option> \n+            </param>\n+        </when>\n+    </conditional>\n+    <param name=\"random_seed\" type=\"integer\" value=\"1234567890\" label=\"Random\n+        seed used for the parsimony inferences\" help=\"(--random_seed)\"/>\n+    <conditional name=\"selExtraOpts\">\n+        <param name=\"extraOptions\" type=\"select\" label=\"RAxML options to use\"\n+            help=\"The required minimal settings are the input file and the\n+            substitution model. To specify extra options select the 'Full option list'\">\n+            <option value=\"required\">Required options only</option>\n+            <option value=\"full\">Full option list</option>\n+        </param>","path":"tools/raxml/raxml.xml","position":247,"original_position":247,"commit_id":"fcc7cc2846c99920856223fc2b007df218ce3cf8","original_commit_id":"fcc7cc2846c99920856223fc2b007df218ce3cf8","user":{"login":"nsoranzo","id":4924623,"avatar_url":"https://avatars.githubusercontent.com/u/4924623?v=3","gravatar_id":"","url":"https://api.github.com/users/nsoranzo","html_url":"https://github.com/nsoranzo","followers_url":"https://api.github.com/users/nsoranzo/followers","following_url":"https://api.github.com/users/nsoranzo/following{/other_user}","gists_url":"https://api.github.com/users/nsoranzo/gists{/gist_id}","starred_url":"https://api.github.com/users/nsoranzo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nsoranzo/subscriptions","organizations_url":"https://api.github.com/users/nsoranzo/orgs","repos_url":"https://api.github.com/users/nsoranzo/repos","events_url":"https://api.github.com/users/nsoranzo/events{/privacy}","received_events_url":"https://api.github.com/users/nsoranzo/received_events","type":"User","site_admin":false},"body":"Add:\r\n```\r\n<when value=\"required\" />\r\n```","created_at":"2015-11-24T17:19:19Z","updated_at":"2015-11-24T17:19:19Z","html_url":"https://github.com/galaxyproject/tools-iuc/pull/372#discussion_r45765953","pull_request_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/372","_links":{"self":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments/45765953"},"html":{"href":"https://github.com/galaxyproject/tools-iuc/pull/372#discussion_r45765953"},"pull_request":{"href":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/372"}}},"pull_request":{"url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/372","id":49855484,"html_url":"https://github.com/galaxyproject/tools-iuc/pull/372","diff_url":"https://github.com/galaxyproject/tools-iuc/pull/372.diff","patch_url":"https://github.com/galaxyproject/tools-iuc/pull/372.patch","issue_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/372","number":372,"state":"open","locked":false,"title":"RAxML support for Galaxy","user":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"body":"As per the subject, this adds RAxML support for Galaxy. Based on original work by @moskalenko, which I updated a little bit.","created_at":"2015-11-05T17:37:00Z","updated_at":"2015-11-24T17:19:19Z","closed_at":null,"merged_at":null,"merge_commit_sha":"a38e3fd7e99164bc73c2fd05cc90164ebb8aad54","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/372/commits","review_comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/372/comments","review_comment_url":"https://api.github.com/repos/galaxyproject/tools-iuc/pulls/comments{/number}","comments_url":"https://api.github.com/repos/galaxyproject/tools-iuc/issues/372/comments","statuses_url":"https://api.github.com/repos/galaxyproject/tools-iuc/statuses/fcc7cc2846c99920856223fc2b007df218ce3cf8","head":{"label":"tiagoantao:master","ref":"master","sha":"fcc7cc2846c99920856223fc2b007df218ce3cf8","user":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"repo":{"id":45627569,"name":"tools-iuc","full_name":"tiagoantao/tools-iuc","owner":{"login":"tiagoantao","id":34787,"avatar_url":"https://avatars.githubusercontent.com/u/34787?v=3","gravatar_id":"","url":"https://api.github.com/users/tiagoantao","html_url":"https://github.com/tiagoantao","followers_url":"https://api.github.com/users/tiagoantao/followers","following_url":"https://api.github.com/users/tiagoantao/following{/other_user}","gists_url":"https://api.github.com/users/tiagoantao/gists{/gist_id}","starred_url":"https://api.github.com/users/tiagoantao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tiagoantao/subscriptions","organizations_url":"https://api.github.com/users/tiagoantao/orgs","repos_url":"https://api.github.com/users/tiagoantao/repos","events_url":"https://api.github.com/users/tiagoantao/events{/privacy}","received_events_url":"https://api.github.com/users/tiagoantao/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/tiagoantao/tools-iuc","description":"Tool 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