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1 <tool id="make_phylogeny" name="make_phylogeny" version="2.0.0">
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2 <description>Make Phylogeny</description>
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3 <requirements>
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4 <requirement type="binary">make_phylogeny.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_inputdir='$__new_file_path__'
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9 --galaxy_ext_change='$input_fp'
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10 --galaxy_new_ext='fasta'
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11 make_phylogeny.py
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12 --input_fp='$__new_file_path__'/temporary.fasta
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13 --tree_method=$tree_method
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14 --result_fp=$result_fp
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15 --log_fp=$log_fp
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16 --root_method=$root_method</command>
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17 <inputs>
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18 <param name="input_fp" type="data" format="align" label="input_fp"
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19 help="Path to read input alignment (output from filter_alignment) [REQUIRED]"/>
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20 <param name="tree_method" type="select" label="tree_method"
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21 help="Method for tree building. [default: fasttree]">
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22 <option value="clearcut">clearcut</option>
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23 <option value="clustalw">clustalw</option>
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24 <option value="raxml">raxml</option>
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25 <option value="fasttree_v1">fasttree_v1</option>
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26 <option value="fasttree" selected="true">fasttree</option>
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27 <option value="muscle">muscle</option>
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28 </param>
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29 <param name="root_method" type="select" label="root_method"
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30 help="method for choosing root of phylo tree [default: tree_method_default]">
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31 <option value="tree_method_default" selected="true">tree_method_default</option>
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32 <option value="midpoint">midpoint</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
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37 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
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38 </outputs>
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39 <tests>
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40 </tests>
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41 <help>For more information, see make_phylogeny_ in the Qiime documentation.
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42
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43 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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44
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45 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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46
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47 .. _make_phylogeny: http://qiime.org/scripts/make_phylogeny.html</help>
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48 </tool>
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