annotate phylogenies/phytab_raxml_using_ptree.serial.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_useMPtrees" name="Phytab RAxML using Starting trees" version="1">
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2 <description>Phytab RAxML - optimize branch lengths on trees</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_using_ptree.serial.py -i $phytabinput -e $evo -f $efile -t $startingPtreelist> $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="phytabinput" type="data" label="PHYTAB sequence file"/>
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11 <param format="tabular" name="startingPtreelist" type="data" label="Starting trees" help="(e.g., tree list output from PHYTAB RAxML Parsimony.)"/>
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12 <param name="evo" type="select" format="text">
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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
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15 value="PROTGAMMAJTT">PROTGAMMAJTT</option> <option value="PROTGAMMAMTREV">PROTGAMMAMTREV</option> <option value="PROTGAMMAWAG">PROTGAMMAWAG</option> <option
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16 value="PROTGAMMARTREV">PROTGAMMARTREV</option> <option value="PROTGAMMACPREV">PROTGAMMACPREV</option> <option value="PROTGAMMAVT">PROTGAMMAVT</option> <option
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17 value="PROTGAMMABLOSUM62">PROTGAMMABLOSUM62</option> <option value="PROTGAMMAMTMAM">PROTGAMMAMTMAM</option> <option value="PROTGAMMALG">PROTGAMMALG</option> <option
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18 value="PROTGAMMAMTART">PROTGAMMAMTART</option> <option value="PROTGAMMAMTZOA">PROTGAMMAMTZOA</option> <option value="PROTGAMMAPMB">PROTGAMMAPMB</option> <option
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19 value="PROTGAMMAHIVB">PROTGAMMAHIVB</option> <option value="PROTGAMMAHIVW">PROTGAMMAHIVW</option> <option value="PROTGAMMAJTTDCMUT">PROTGAMMAJTTDCMUT</option> <option
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20 value="PROTGAMMAFLU">PROTGAMMAFLU</option> <option value="PROTGAMMAGTR">PROTGAMMAGTR</option>
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21 </param>
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22 <param format="txt" name="efile" type="data" optional="true" value="n" label="Tab seperated file with partition name in first column, evolutionary model in the second column. Must be RAxML
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23 valid model names. (optional)"/>
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24
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25 </inputs>
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26 <outputs>
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27 <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
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28 <data format="tabular" name="results.phy" label="${tool.name} on ${on_string}: results" from_work_dir="results/results.phy" />
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29 </outputs>
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30 <tests>
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31 </tests>
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32 <help>
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33
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34 **What it does**
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35
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36 This tool estimates likelihood trees and branch lengths for a PHYTAB file using starting trees (e.g., parsimony trees) to accelerate tree estimation.
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37
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38 **Input requirements**
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39
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40 1. PHYTAB sequence file
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41 2. Starting tree list: two tab-delimited columns with the partition(gene) name and its newick starting tree (generated by PHYTAB RAxML-Parsimony)::
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42
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43 geneA (((Species_a,Species_b),Species_c),Species_d);
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44 geneB ((Species_a,Species_b),(Species_c,Species_d));
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45
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46 </help>
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47 </tool>
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48