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annotate upgma_cluster.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_upgma_cluster" name="upgma cluster" version="1.9.1galaxy1">
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2 <description>Build a UPGMA tree comparing samples</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements" />
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10 <command>
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11 <![CDATA[
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12 upgma_cluster.py
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13 -i upgma_cluster_input
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14 -o upgma_cluster_output
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15 ]]>
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16 </command>
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18 <inputs>
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19 <param label="-i/--input_path: input path. directory for batch processing,
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20 filename for single file operation" name="input_path" type="data"/>
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21 </inputs>
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23 <outputs>
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24 <data format="newick" name="output_tree"/>
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25 </outputs>
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27 <tests>
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28 <test>
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29 </test>
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30 </tests>
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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32 <help><![CDATA[
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33 **What it does?**
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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35 In addition to using PCoA, it can be useful to cluster samples using UPGMA (Unweighted Pair Group Method with Arithmetic mean, also known as average linkage). As with PCoA, the input to this step is a distance matrix (i.e. resulting file from beta_diversity.py).
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36 The output is a newick formatted tree compatible with most standard tree viewing programs. Batch processing is also available, allowing the analysis of an entire directory of distance matrices.
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37 ]]>
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38 </help>
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40 <citations>
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41 <expand macro="citations" />
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42 </citations>
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43 </tool>