Mercurial > repos > iuc > qiime_upgma_cluster

annotate upgma_cluster.xml @ 2:9f73c09cef36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit e5d24fc90f811c8994ec8b72371ab4100d2c294c
author iuc
date Fri, 19 May 2017 04:12:32 -0400
parents e7324235f49e
children 4e9b6a0fcb78
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e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_upgma_cluster" name="Build UPGMA tree" version="@WRAPPER_VERSION@.0">
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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2 <description>comparing samples</description>
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3 <macros>
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4 <import>macros.xml</import>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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5 </macros>
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6 <expand macro="requirements"/>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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7 <version_command>upgma_cluster.py -v</version_command>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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8 <command detect_errors="aggressive"><![CDATA[
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9 mkdir input
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10 &&
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11 #for $i, $matrix in enumerate($input_path)
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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12 cp '$matrix' 'input/dataset_$i' &&
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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13 #end for
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14 upgma_cluster.py
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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15 --input_path input
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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16 --output_path output
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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17 ]]></command>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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18 <inputs>
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19 <param argument="--input_path" type="data" format="txt" label="Distance matrix" multiple="true"/>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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20 </inputs>
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21 <outputs>
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22 <collection type="list" name="output_trees" label="${tool.name} on ${on_string}: UPGMA trees">
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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23 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tre" directory="output"/>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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24 </collection>
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25 </outputs>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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26 <tests>
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27 <test>
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28 <param name="input_path" value="upgma_cluster/beta_div_1.txt,upgma_cluster/beta_div_2.txt,upgma_cluster/beta_div_3.txt,upgma_cluster/beta_div_4.txt"/>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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29 <output_collection name="output_trees" type="list" count="4">
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30 <element name="upgma_dataset_0">
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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31 <assert_contents>
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32 <has_text text="PC.636" />
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33 </assert_contents>
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34 </element>
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35 <element name="upgma_dataset_3">
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36 <assert_contents>
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37 <has_text text="PC.355" />
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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38 </assert_contents>
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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39 </element>
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40 </output_collection>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 **What it does**
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45
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46 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).
e7324235f49e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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47 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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48 ]]></help>
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49 <citations>
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50 <expand macro="citations"/>
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51 </citations>
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52 </tool>