Mercurial > repos > iuc > qiime_upgma_cluster

annotate upgma_cluster.xml @ 5:4e9b6a0fcb78 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:33:48 -0400
parents e7324235f49e
children aae131716d22
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4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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1 <tool id="qiime_upgma_cluster" name="Build a UPGMA tree" version="@WRAPPER_VERSION@.0">
4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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2 <description> comparing samples (upgma_cluster)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>upgma_cluster.py -v</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 mkdir input
4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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10 &&
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11 #for $i, $matrix in enumerate($input_path)
4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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12 cp '$matrix' 'input/dataset_$i' &&
4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 #end for
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14 upgma_cluster.py
4e9b6a0fcb78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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15 --input_path input
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16 --output_path output
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input_path" type="data" format="txt" multiple="true" label="Distance matrix"/>
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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">
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23 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tre" directory="output"/>
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24 </collection>
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25 </outputs>
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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">
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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" />
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38 </assert_contents>
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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).
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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>