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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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1 <tool id="alpha_diversity" name="alpha_diversity" version="1.2.0">
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2 <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description>
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3 <requirements>
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4 <requirement type="binary">alpha_diversity.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 alpha_diversity.py
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9 --input_path=$input_path
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10 --output_path=$output_path
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11 --metrics=$metrics
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12 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
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13 --tree_path=$tree_path
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14 #end if
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15
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16 </command>
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17 <inputs>
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18 <param name="input_path" type="data" format="tabular" label="OTU table"
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19 help="input path. directory for batch processing, filename for single file operation"/>
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20 <param name="metrics" type="select" multiple="true" label="metrics"
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21 help="metrics to use">
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22 <option value="ACE">ACE</option>
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23 <option value="berger_parker_d">berger_parker_d</option>
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24 <option value="brillouin_d">brillouin_d</option>
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25 <option value="chao1">chao1</option>
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26 <option value="chao1_confidence">chao1_confidence</option>
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27 <option value="dominance">dominance</option>
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28 <option value="doubles">doubles</option>
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29 <option value="equitability">equitability</option>
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30 <option value="fisher_alpha">fisher_alpha</option>
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31 <option value="heip_e">heip_e</option>
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32 <option value="kempton_taylor_q">kempton_taylor_q</option>
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33 <option value="margalef">margalef</option>
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34 <option value="mcintosh_d">mcintosh_d</option>
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35 <option value="mcintosh_e">mcintosh_e</option>
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36 <option value="menhinick">menhinick</option>
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37 <option value="michaelis_menten_fit">michaelis_menten_fit</option>
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38 <option value="observed_species">observed_species</option>
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39 <option value="osd">osd</option>
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40 <option value="reciprocal_simpson">reciprocal_simpson</option>
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41 <option value="robbins">robbins</option>
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42 <option value="shannon">shannon</option>
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43 <option value="simpson">simpson</option>
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44 <option value="simpson_e">simpson_e</option>
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45 <option value="singles">singles</option>
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46 <option value="strong">strong</option>
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47 <option value="PD_whole_tree">PD_whole_tree</option>
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48 </param>
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49 <param name="tree_path" type="data" format="tre" label="tree_path" optional="true"
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50 help="path to newick tree file, required for phylogenetic metrics: PD_whole_tree"/>
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51 </inputs>
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52 <outputs>
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53 <data format="tabular" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity"/>
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54 </outputs>
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55 <tests>
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56 </tests>
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57 <help>
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58
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59 </help>
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60 </tool>
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