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comparison qiime/principal_coordinates.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="principal_coordinates" name="principal_coordinates" version="1.2.0">
2 <description>Principal Coordinates Analysis (PCoA)</description>
3 <requirements>
4 <requirement type="binary">principal_coordinates.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 principal_coordinates.py
9 --input_path=$input_path
10 --output_path=$output_path
11 </command>
12 <inputs>
13 <conditional name="run_type">
14 <param name="input_type" type="select" label="Input Type" help="Select the type/number of input file(s). If you want to process multiple diversity metrics, select 'multiple files.'">
15 <option value="single">Single File</option>
16 <option value="multi">Multiple Files</option>
17 </param>
18 <when value="single">
19 <param name="input_path" type="data" format="qiimedistmat" label="input_path"
20 help="path to the input distance matrix file (i.e., the output from beta_diversity.py). [REQUIRED]"/>
21 </when>
22 <when value="multi">
23 <param name="input_path" type="data" format="qiimedistmat" label="input_path"
24 help="Path to the first distance matrix file of the metrics run. Example: if you ran beta diversity for both 1: unweighted and 2: weighted unifrac, choose the unweighted file. [REQUIRED]"/>
25 </when>
26 </conditional>
27 </inputs>
28 <outputs>
29 <data format="qiimepca" name="output_path" label="${tool.name} on ${on_string}: coordinates"/>
30 </outputs>
31 <tests>
32 </tests>
33 <help>For more information, see principle_coordinates_ in the Qiime documentation.
34
35 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
36 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
37
38 .. _principle_coordinates: http://qiime.org/scripts/principal_coordinates.html</help>
39 </tool>
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