| Previous changeset 3:df98a0425c8d (2015-12-11) |
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Commit message:
Uploaded |
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modified:
fastme.xml |
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| diff -r df98a0425c8d -r aea74cec21e0 fastme.xml --- a/fastme.xml Fri Dec 11 09:51:04 2015 -0500 +++ b/fastme.xml Fri Apr 22 08:04:53 2016 -0400 |
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| b'@@ -1,193 +1,201 @@\n-<tool id="sniplay_fastme" name="Fastme" version="1.1.0">\n- \n- <!-- [REQUIRED] Tool description displayed after the tool name -->\n- <description> Calculate distance tree for an alignment file</description>\n- \n- <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->\n+<tool id="fastme" name="FastME" version="2.1.4.2">\n+ <description>Distance-based inference of phylogenetic trees</description>\n <requirements>\n- <requirement type="binary">perl</requirement>\n-\t<requirement type="package" version="2.1.4">fastme</requirement>\n+ <requirement type="package" version="2.1.4">fastme</requirement>\n </requirements>\n- \n- <!-- [STRONGLY RECOMMANDED] Exit code rules -->\n+ <version_command>\n+ <![CDATA[ fastme --version ]]>\n+ </version_command>\n <stdio>\n- <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->\n <exit_code range="1:" level="fatal" />\n </stdio>\n+ <command>fastme --input_data=$input\n+ --output_tree=$outputTree\n+ --output_matrix=$outputMatrix\n+ --output_info=$outputLog\n+ --nb_threads=\\${GALAXY_SLOTS:-1}\n \n- \n- <!-- [REQUIRED] The command to execute -->\n- <command>\n-\tfastme --input_data=$input_data --dna=$model --output_tree=$fileout \n-\t#if str( $distance ) == "SPR":\n-\t--spr\n-\t#elif str( $distance )[:3] == "NNI" :\n-\t #if str( $distance ) == "NNI_B" :\n- --nni=B\n- #else :\n- --nni=O\n- #end if\n+ #if $typeChoice.datatype =="d"\n+ --dna=$typeChoice.modeldna\n+\n+ #else if $typeChoice.datatype =="p"\n+ --protein=$typeChoice.modelprot\n+\n+ #else if $typeChoice.datatype =="cfg":\n+ ## Read information of sequence type\n+ ## read an info file to choose which option set and set a model by default\n+ #set $info = open( str($input_info) ).read()\n+ #if \'dna\' in $info:\n+ --dna=T\n+ #else if \'protein\' in $info:\n+ --protein=L\n+ #end if\n+ #end if\n+\n+ #if $gammaChoice.gamma == "true"\n+ --gamma=$gammaChoice.rate\n+ #end if\n+\n+ $distance\n+ $equilibrium\n+ $removeGap\n+ $treeRefinement\n+\n+ #if $bootChoice.boot == "true"\n+ --output_boot=$outputBoostrap\n+ --bootstrap=$bootChoice.replicates\n+ #end if\n+\n+ >> tmp_stdout;\n+ cat tmp_stdout > $outputLog;\n \n-\t#else :\n-\t--method=$distance\n-\t#end if\n-\t> $fileout_log\n </command>\n- \n-\n-\n- <!-- [REQUIRED] Input files and tool parameters -->\n <inputs>\n-\t<param name="input_data" type="data" format="txt" optional="false" label="Phylip input" />\n-\t<param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />\n-\t<param name="model" type="select" label="Evolutionary model" >\n-\t <option value="p">p-distance</option>\n-\t <option value="Y">RY symetric</option>\n-\t <option value="R">RY</option>\n-\t <option value="J">JC69</option>\n-\t <option value="K">K2P</option>\n-\t <option value="1">F81</option>\n-\t <option value="4" selected="true">F84</option>\n-\t <option value="T">TN93</option>\n-\t <option value="L">LogDet</option>\n+ <param name="input" type="data" format="phylip, phy" label="Fastme input" help="Phylip Alignment or Matrix file"/>\n+ <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" />\n+ <conditional '..b'titution model.\n+ Use this option if you whish to estimate the amino-acid frequencies\n+ by counting their occurence in the input alignment.\n+\n+ -g alpha, --gamma=alpha\n+ Use this option if you wish to have gamma distributed rates across sites.\n+ By default, FastME runs with no gamma variation.\n+ If running FastME with gamma distributed rates across sites, the [alpha] default value is 1.0.\n+ Only helpful when the input data file contains sequences alignment(s).\n+\n+ -n NNI, --nni=NNI\n+ Use this option to do [NNI] tree topology improvement.\n+ You may choose the [NNI] type from:\n+ NNI_(B)alME (default) or NNI_(O)LS.\n+\n+ -s, --spr\n+ Use this option to do SPR tree topology improvement.\n+\n+ -w branch, --branch_length=branch\n+ Use this option to indicate the branch length to assign to the tree.\n+ Only helpful when not improving the tree topology (no NNI nor SPR).\n+ You may choose the branch length from:\n+ (B)alLS (default), (O)LS or (n)one. (n)one is only available with BIONJ, NJ or UNJ.\n \n-\t(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...\n-\t\n+ -D datasets, --datasets=datasets\n+ Use this option to indicate the number of datasets in your input\n+ data file. Default value is 1.\n+\n+ -b replicates, --bootstrap=replicates\n+ Use this option to indicate the number of replicates FastME will\n+ do for bootstrapping. Default value is 0.\n+ Only helpful when the input data file contains sequences alignment(s).\n+\n+ -z seed, --seed=seed\n+ Use this option to initialize randomization with seed value. Only helpful when bootstrapping.\n+\n+ -c Use this option if you want FastME only to compute distance matrix.\n+ Only helpful when the input data file contains sequences alignment(s).\n+\n+ -T number_of_threads, --nb_threads=number_of_threads\n+ Use this option to set the number of threads to use.\n+ Default number of threads is 4.\n+\n+ -v value, --verbose=value\n+ Sets the verbose level to value [0-3]. Default value is 0\n+\n+ -V, --version\n+ Prints the FastME version.\n+\n+ -h, --help Display this usage.\n+\n+\n+For further informations, please visite FastME_\n+\n+.. _FastME: http://www.atgc-montpellier.fr/fastme/usersguide.php\n \n </help>\n- \n <citations>\n- <!-- [HELP] As DOI or BibTex entry -->\n- <citation type="bibtex"> \n-@article{Lefort30062015,\n-author = {Lefort, Vincent and Desper, Richard and Gascuel, Olivier}, \n-title = {FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program},\n-year = {2015}, \n-doi = {10.1093/molbev/msv150}, \n-abstract ={FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).}, \n-URL = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.abstract}, \n-eprint = {http://mbe.oxfordjournals.org/content/early/2015/07/25/molbev.msv150.full.pdf+html}, \n-journal = {Molecular Biology and Evolution} \n-}\n-\n-\t</citation>\n-\n+ <citation type="doi">10.1093/molbev/msv150</citation>\n+ <citation type="doi">10.1089/106652702761034136</citation>\n </citations>\n-\n-\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |