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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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1 <tool id="make_phylogeny" name="make_phylogeny" version="1.2.0">
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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 make_phylogeny.py
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9 --input_fp=$input_fp
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10 --tree_method=$tree_method
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11 --root_method=$root_method
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12 --result_fp=$result_fp
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13 --log_fp=$log_fp
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14 </command>
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15 <inputs>
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16 <param name="input_fp" type="data" format="align" label="input_fp"
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17 help="Path to read input alignment [REQUIRED]"/>
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18 <param name="tree_method" type="select" label="tree_method"
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19 help="Method for tree building. Valid choices are: clearcut, clustalw, raxml, fasttree_v1, fasttree, muscle [default: fasttree]">
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20 <option value="clearcut">clearcut</option>
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21 <option value="clustalw">clustalw</option>
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22 <option value="raxml">raxml</option>
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23 <option value="fasttree_v1">fasttree_v1</option>
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24 <option value="fasttree" selected="true">fasttree</option>
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25 <option value="muscle">muscle</option>
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26 </param>
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27 <param name="root_method" type="select" label="root_method"
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28 help="method for choosing root of phylo tree Valid choices are: midpoint, tree_method_default [default: tree_method_default]">
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29 <option value="tree_method_default" selected="true">tree_method_default</option>
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30 <option value="midpoint">midpoint</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
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35 <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help>
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40
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41 </help>
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42 </tool>
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