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annotate phylographics/tab2trees.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="tab2trees" name="tab2trees" version="1.0.0">
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2 <description>Create PDF file of phylogeny graphics from table of tree names and Newick trees</description>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 <command interpreter="bash">tab2trees.sh $input $output $treetype $extips $labeltax $Rfile $query $midpoint</command>
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4 <inputs>
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5 <param name="input" type="data" format="tabular" label="Dataset" help="First column=Tree Name. Second column=Newick phylogeny"/>
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6 <param name="treetype" type="select" label="Tree Plotting Style">
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7 <option value="phylogram">phylogram</option>
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8 <option value="cladogram">cladogram</option>
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9 <option value="fan">fan</option>
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10 <option value="unrooted">unrooted</option>
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11 <option value="radial">radial</option>
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12 </param>
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13 <param name='extips' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Exclude Tip Labels'/>
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14 <param name='query' type='boolean' checked='false' truevalue='yes' falsevalue='no' label='Highlight genes with QUERY and LANDMARK1 in name using Tip Label'/>
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15 <param format="tabular" name="labeltax" type="data" optional="true" label="Species to Mark File" help="Tab delimited file with 2 columns, gene, species. These will be marked on the trees." />
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16 <param name='midpoint' type='boolean' checked='true' truevalue='yes' falsevalue='no' label='Midpoint Root all Trees'/>
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="Rfile" />
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20 <data format="pdf" name="output" />
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21 </outputs>
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22
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23 <help>
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24 **What it does**
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25
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26 Creates a "book" of multiple phylogenetic tree graphics, one per page, in pdf format.
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27
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28 ------
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29
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30 **Inputs**
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31
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32 tab delimited file. Column 1 is tree name column 2 is newick tree string.
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33
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34 ------
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35
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36 **Outputs**
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37
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38 PDF file of phylogeny graphics.
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39
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40 -------
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41
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42 **Additional Information**
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43
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44 Please direct questions or comments to ucsb_phylogenetics@lifesci.ucsb.edu or, if you can, enter them on the
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45 osiris_phylogenetics site at bitbucket.org
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46
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47 -------
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48
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49 **Citations**
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50
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51 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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52
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53 Current Osiris Citation is here
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54
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55 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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56 </help>
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57 </tool>