Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phylogenies/raxml_pars.xml @ 0:5b9a38ec4a39 draft default tip
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| author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
|---|---|
| date | Tue, 11 Mar 2014 12:19:13 -0700 |
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| -1:000000000000 | 0:5b9a38ec4a39 |
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| 1 <tool id="raxml_pars" name="raxml_pars" version="1.0.0" force_history_refresh='True'> | |
| 2 <description> Use RAxML to calculate a phylogeny with Parsimony </description> | |
| 3 <requirements> | |
| 4 <requirement type="package">raxml</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="perl"> | |
| 7 raxml_pars.pl $datatype $data_file $part_file | |
| 8 $seed $Out > $raxml_log | |
| 9 2>&1 | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param format="phylip" name="data_file" type="data" label="Raxml Phylip File" help=""/> | |
| 13 <param name="Out" type="text" label="Outgroup (optional)" help="The name of one or more (comma-separated) outgroup(s) can be specified"/> | |
| 14 <param name="datatype" type="select" label="Data Type" help="If you have multiple, mixed data types, specify them in a partition file "> | |
| 15 <option value="PROTGAMMAWAG">PROTEIN</option> | |
| 16 <option value="GTRGAMMA">DNA</option> | |
| 17 <option value="BINGAMMA">BINARY</option> | |
| 18 <option value="MULTIGAMMA">Multistate Morphology</option> | |
| 19 </param> | |
| 20 <param name="seed" type="integer" value="1234567" label="Random Number Seed for search"/> | |
| 21 <param format="txt" name="part_file" type="data" optional="true" label="Partition file" help="You may provide an alignment partition file."/> | |
| 22 <param name="Run" type="text" label="Run Name" help="For Galaxy History"/> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="txt" name="raxml_log" label="$Run: ${tool.name} Screen Output on ${on_string}" /> | |
| 26 <data format="txt" name="raxml_info" label="$Run: ${tool.name} Log File on ${on_string}" from_work_dir="RAxML_info.parsimony" /> | |
| 27 <data format="txt" name="best_trees" label="$Run: ${tool.name} MP Tree ${on_string}" from_work_dir="RAxML_parsimonyTree.parsimony" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 </tests> | |
| 31 <help> | |
| 32 **What it does** | |
| 33 | |
| 34 RAxML_pars estimates phylogenetic trees, in this case calling a Parsimony algorithm. | |
| 35 | |
| 36 ------ | |
| 37 | |
| 38 **Inputs** | |
| 39 | |
| 40 Input file is a RAxML compatible text file. This can be generated by Osiris tools from an aligned fasta file with fasta2phylipE or from a PHYTAB format file with phylocatenator. | |
| 41 | |
| 42 ------ | |
| 43 | |
| 44 **Outputs** | |
| 45 | |
| 46 RAxML writes the resulting tree file in newick text format, which can be viewed in Osiris with TreeVector (of the mothur package). | |
| 47 | |
| 48 ------- | |
| 49 | |
| 50 **Additional Information** | |
| 51 | |
| 52 raxml Home Page. | |
| 53 http://www.exelixis-lab.org/software.html | |
| 54 | |
| 55 ------- | |
| 56 | |
| 57 **Citations** | |
| 58 | |
| 59 This tool is part of the Osiris Phylogenetics Tool Package for Galaxy. If you make extensive use of this tool in a publication, please consider citing the following. | |
| 60 | |
| 61 Current Osiris Citation is here | |
| 62 | |
| 63 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html | |
| 64 | |
| 65 Additional Citations for this tool | |
| 66 | |
| 67 Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. | |
| 68 http://bioinformatics.oxfordjournals.org/content/22/21/2688.short | |
| 69 | |
| 70 </help> | |
| 71 </tool> | |
| 72 | |
| 73 |