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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 <tool id="phytab_raxml" name="Phytab RAxML" version="1.1">
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2 <description> for phytab input</description>
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3 <requirements>
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4 <requirement type="package">raxml</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 phytab_raxml.py -i $sequence -e $evo -f $efile -T 4 > $stdout 2>&amp;1
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8 </command>
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9 <!-- if using a queuing system, make sure number of ppn in jobrunner matches threads as set above -->
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10 <inputs>
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11 <param format="tabular" name="sequence" type="data" label="PHYTAB sequence file"/>
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12 <param name="evo" type="select" format="txt">
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13 <label>Model of evolution to apply to all data partitions (-m)</label>
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14 <option value="GTRGAMMA">GTRGAMMA</option> <option value="PROTGAMMADAYHOFF">PROTGAMMADAYHOFF</option> <option value="PROTGAMMADCMUT">PROTGAMMADCMUT</option> <option value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
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15 </param>
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16 <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab-delimited file with partition name in first column, evolutionary model in the second column. Must be RAxML
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17 valid model names. (optional)"/>
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18 </inputs>
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19 <outputs>
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20 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
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21 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
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22 </outputs>
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23 <tests>
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24 </tests>
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25 <help>
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26 **What it does**
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27 Accepts Phytab input file (one or multiple gene partitions). Runs RAxML using specified model or model file for each partition.
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28
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29 For phytab format description, see: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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30
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31 See RAxML for additional information: https://github.com/stamatak/standard-RAxML
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32
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33 -------
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34 **Performance**
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35 The extent to which runs are parallelized may be altered through the Galaxy jobrunner (command-line). The number of threads is set in this tool's XML command section.
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36
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37 -------
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38 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the osiris_phylogenetics site at bitbucket.org
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39
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40 -------
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41
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42 **Citations**
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43
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44 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.
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45
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46 Current Osiris Citation is here
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47
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48 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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49
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50 </help>
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51 </tool>
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52