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Commit message:
planemo upload commit b361f9ed82802229277cad4433f3de57f54a06f9 |
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modified:
mrbayes.xml |
| b |
| diff -r 2fe97192eb4b -r bd2c8053e155 mrbayes.xml --- a/mrbayes.xml Fri Dec 18 14:21:08 2015 -0500 +++ b/mrbayes.xml Wed Sep 20 12:11:19 2017 -0400 |
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| b'@@ -1,148 +1,158 @@\n <?xml version="1.0"?>\n-<tool id="mrbayes" name="MrBayes" version="1.0.1">\n- <description>with options and commands</description>\n- <requirements>\n- <requirement type="package" version="3.2.6">mrbayes</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>\n- </stdio>\n- <command> mb $command_file > $outfile\n-## print list of avaialble variables\n-#silent sys.stderr.write("\\n \\n \\n ======== Cheetah template variables ========\\n")\n-#for k,v in $searchList[2].items()\n-#silent sys.stderr.write(" %s = %s\\n" % (str(k), str(v) ))\n-#end for\n-#silent sys.stderr.write("======== End of Cheetah template variables ========\\n \\n \\n")\n- </command>\n- <configfiles>\n- <configfile name="command_file">\n- begin mrbayes;\n- set Seed=$seed;\n- set Swapseed=$swapseed;\n- set quitonerror=yes;\n- execute $data;\n- outgroup $outgroup;\n- $model;\n- lset rates=$rates;\n-#if str($filename) != ""\n- mcmcp filename=$filename;\n-#end if#\n- mcmcp ngen=$ngen nrun=$nrun nchain=$nchain checkfreq=$checkfreq samplefreq=$samplefreq printfreq=$printfreq stoprule=$stoprule burninfrac=$burninfrac;\n-#if int($ngen) >= int($checkfreq)\n- $append;\n-#end if#\n- mcmc;\n- $sump\n- $sumt\n-#if str($plot) == "plot"\n- plot;\n-#end if#\n- end;\n- </configfile>\n- </configfiles>\n- <inputs>\n- <param name="data" type="data" format="nex" label="Nexus input file"/>\n+<tool id="mrbayes" name="MrBayes" version="1.0.2">\n+ <description>with options and commands</description>\n+ <requirements>\n+ <requirement type="package" version="3.2.6">mrbayes</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>\n+ </stdio>\n+ <command>mb $command_file > $outfile\n+ ## print list of avaialble variables\n+ #silent sys.stderr.write("\\n \\n \\n ======== Cheetah template variables ========\\n")\n+ #for k,v in $searchList[2].items()\n+ #silent sys.stderr.write(" %s = %s\\n" % (str(k), str(v) ))\n+ #end for\n+ #silent sys.stderr.write("======== End of Cheetah template variables ========\\n \\n \\n")\n+ </command>\n+ <configfiles>\n+ <configfile name="command_file">\n+ begin mrbayes;\n+ set Seed=$seed;\n+ set Swapseed=$swapseed;\n+ set quitonerror=yes;\n+ execute $data;\n+ outgroup $outgroup;\n+ $model;\n+ lset rates=$rates;\n+ #if str($filename) != ""\n+ mcmcp filename=$filename;\n+ #end if\n+ mcmcp ngen=$ngen\n+ nrun=$nrun\n+ nchain=$nchain\n+ checkfreq=$checkfreq\n+ samplefreq=$samplefreq\n+ printfreq=$printfreq\n+ stoprule=$stoprule\n+ burninfrac=$burninfrac;\n+ #if int($ngen) >= int($checkfreq)\n+ $append;\n+ #end if\n+ mcmc;\n+ $sump\n+ $sumt\n+ #if str($plot) == "plot"\n+ plot;\n+ #end if\n+ end;\n+ </configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="data" type="data" format="nex" label="Nexus input file"/>\n \n- <param name="filename" type="text" label="Output filename" size="10" value=""\n- help="Output files will be named this with .p, .t, .mcmc extensions. Use to avoid overwriting files when running repeated analyses on the same dataset." />\n+ <param name="filename" type="text" label="Output filename" size="10" value=""\n+ help="Output files will be named this with .p, .t, .mcmc extensions. Use to avoid overwriting files when running repeated analyses on the same dataset."/>\n \n- <param name="ngen" type="integer" label="<hr>Number of gen'..b'a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.\n+MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and\n+evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution\n+of model parameters.\n \n See the manual_ or the `command reference`_ for more information.\n \n@@ -163,17 +175,18 @@\n \n Models are defined by the following MrBayes options::\n \n- GRT: lset nst=6;\n- SYM: lset nst=6; prset statefreqpr=fixed(equal);\n- HKY: lset nst=2;\n- K2P: lset nst=2; prset statefreqpr=fixed(equal);\n- F81: lset nst=1;\n- JC: lset nst=1; prset statefreqpr=fixed(equal);\n- Mixed: lset nst=mixed;\n+GTR: lset nst=6;\n+SYM: lset nst=6; prset statefreqpr=fixed(equal);\n+HKY85: lset nst=2;\n+K2P: lset nst=2; prset statefreqpr=fixed(equal);\n+F81: lset nst=1;\n+JC69: lset nst=1; prset statefreqpr=fixed(equal);\n+Mixed: lset nst=mixed;\n \n Each model makes different assumptions about nucelotide substitution rates and state frequencies.\n \n-The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by grouping the six rates in various combinations.\n+The mixed model performs Markov chain sampling over the space of all possible reversible substitution models, by\n+grouping the six rates in various combinations.\n \n -----\n \n@@ -181,27 +194,34 @@\n \n **Tip for repetitive analyses**\n \n-Note that running the same analysis on the same dataset in Galaxy will overwrite .p, .t, and .mcmc files for that dataset. This can be avoided by copying the dataset or re-uploading it, or by specifying a new filename.\n+Note that running the same analysis on the same dataset in Galaxy will overwrite .p, .t, and .mcmc files for\n+that dataset. This can be avoided by copying the dataset or re-uploading it, or by specifying a new filename.\n \n .. class:: infomark\n \n **Tip for using append**\n \n-If you want to use the append functionality, all parameters will have to be identical to your initial analysis. The easiest way to ensure this is by using the blue "Run this job again" arrow on the dataset, and checking the additional append box. Note also that ngen will be the total number of generations, not the number of generations to add, so you should increase this value except if a run was interrupted. Selecting append while checkfreq > ngen will have no effect.\n+If you want to use the append functionality, all parameters will have to be identical to your initial analysis.\n+The easiest way to ensure this is by using the blue "Run this job again" arrow on the dataset, and checking the\n+additional append box. Note also that ngen will be the total number of generations, not the number of\n+generations to add, so you should increase this value except if a run was interrupted. Selecting append while\n+checkfreq > ngen will have no effect.\n \n -----\n \n Wrapper originally created by AAFC-MBB -> https://github.com/AAFC-MBB/\n-</help>\n-<citations>\n- <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001,\n- author = {Huelsenbeck JP, Ronquist F.},\n- title = {MRBAYES: Bayesian inference of phylogenetic trees.},\n- journal = {Bioinformatics},\n- year = {2001},\n- volume = {17},\n- pages = {754-755},\n- url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}\n- }</citation>\n-</citations>\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="bibtex">@ARTICLE {huelsenbeckjpronquistf.2001,\n+ author = {Huelsenbeck JP, Ronquist F.},\n+ title = {MRBAYES: Bayesian inference of phylogenetic trees.},\n+ journal = {Bioinformatics},\n+ year = {2001},\n+ volume = {17},\n+ pages = {754-755},\n+ url = {http://www.ncbi.nlm.nih.gov/pubmed/11524383}\n+ }\n+ </citation>\n+ </citations>\n </tool>\n' |