annotate phylostatistics/tree_species.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="tree_species" name="tree_species" version="1.0">
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2 <description>Writes species not in a phylogeny to a text list.</description>
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3 <command interpreter="perl">
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4 tree_species.pl $infile $treefile > $outfile
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5 </command>
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6 <inputs>
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7 <param format="txt" name="infile" type="data" label="Full text list of species."/>
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8 <param format="txt" name="treefile" type="data" label="Tree to search. Newick format."/>
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9 </inputs>
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10 <outputs>
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11 <data format="txt" name="outfile" label="${tool.name} on ${on_string}: stdout" />
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12 </outputs>
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13 <help>
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 **What it does**
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15
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16 This tool can be used to determine which species from a list are not present in a tree.
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17 Searches, one at a time, for species (OTUs) that are present in a tree file. If not found, the species is written to the output file.
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18
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19 ------
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20
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21 **Inputs**
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22
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23 1. A text list of species to use to search.
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24 2. A phylogeny file.
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25
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26 ------
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27
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28 **Outputs**
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29
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30 A text list of species (OTU) names.
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31
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32 -------
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33
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34 **Additional Information**
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35
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36 This is a very simple perl script that just searches a text file for the presence of each line in the other file.
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37
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38 -------
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39
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40 **Citations**
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41
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42 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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43
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44 Current Osiris Citation is here
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45
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46 http://osiris-phylogenetics.blogspot.com/2012/10/citation.html
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47
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48 </help>
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49 </tool>