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author q2d2
date Fri, 13 Jan 2023 22:56:39 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2022.11.1)
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10 for:
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11 qiime2 (version: 2022.11.1)
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12 -->
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13 <tool name="qiime2 gneiss correlation-clustering" id="qiime2__gneiss__correlation_clustering" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Hierarchical clustering using feature correlation.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.11</container>
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17 </requirements>
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18 <version_command>q2galaxy version gneiss</version_command>
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19 <command detect_errors="exit_code">q2galaxy run gneiss correlation_clustering '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples in which the columns will be clustered.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[Frequency]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="pseudocount" type="float" value="0.5" label="pseudocount: Float" help="[default: 0.5] The value to add to zero counts in the feature table."/>
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <data name="clustering" format="qza" label="${tool.name} on ${on_string}: clustering.qza" from_work_dir="clustering.qza"/>
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36 </outputs>
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37 <tests/>
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38 <help>
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39 QIIME 2: gneiss correlation-clustering
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40 ======================================
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41 Hierarchical clustering using feature correlation.
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42
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43
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44 Outputs:
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45 --------
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46 :clustering.qza: A hierarchy of feature identifiers where each tip corresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.
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47
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48 |
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49
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50 Description:
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51 ------------
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52 Build a bifurcating tree that represents a hierarchical clustering of features. The hiearchical clustering uses Ward hierarchical clustering based on the degree of proportionality between features.
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53
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54
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55 |
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56
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57 </help>
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58 <citations>
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59 <citation type="bibtex">@article{cite1,
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60 author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob},
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61 journal = {MSystems},
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62 number = {1},
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63 pages = {e00162--16},
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64 publisher = {Am Soc Microbiol},
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65 title = {Balance trees reveal microbial niche differentiation},
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66 volume = {2},
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67 year = {2017}
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68 }
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69 </citation>
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70 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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71 </citations>
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72 </tool>