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annotate phylogenies/phytab_raxml_small.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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 <tool id="phytab_raxml_small" name="Phytab RAxML SMALL" version="1.0">
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 <description>Phytab RAxML SMALL - RAxML for phytab format. Calls only 1 node for 3 hours</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 <inputs>
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10 <param format="tabular" name="sequence" type="data" label="PHYTAB sequence file"/>
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11 <param name="evo" type="select" format="text">
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12 <label>Model of evolution to apply to all data partitions (-m)</label>
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13 <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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14 </param>
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15 <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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16 valid model names. (optional)"/>
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
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20 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
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21 </outputs>
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22 <tests>
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23 </tests>
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24 <help>
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25 **Parallel RaXML**
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26 See phytab description here: http://osiris-phylogenetics.blogspot.com/2012/09/introduction-to-phytab-format.html
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27 </help>
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28 </tool>
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