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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:48:26 +0000
parents dc55b54f3fac
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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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 gneiss assign-ids" id="qiime2__gneiss__assign_ids" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</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 assign_ids '$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="input_table" type="data" format="qza" label="input_table: FeatureTable[Frequency]" help="[required] The input table of counts.">
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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 <param name="input_tree" type="data" format="qza" label="input_tree: Phylogeny[Rooted]" help="[required] The input tree with potential missing ids.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="Phylogeny[Rooted]"/>
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33 </options>
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data name="output_table" format="qza" label="${tool.name} on ${on_string}: output_table.qza" from_work_dir="output_table.qza"/>
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39 <data name="output_tree" format="qza" label="${tool.name} on ${on_string}: output_tree.qza" from_work_dir="output_tree.qza"/>
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40 </outputs>
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41 <tests/>
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42 <help>
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43 QIIME 2: gneiss assign-ids
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44 ==========================
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45 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
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46
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47
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48 Outputs:
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49 --------
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50 :output_table.qza: A table with features matching the tree tips.
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51 :output_tree.qza: A tree with uniquely identifying ids.
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52
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53 |
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54
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55 Description:
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56 ------------
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57 Assigns UUIDs to uniquely identify internal nodes in the tree. Also corrects for polytomies to create strictly bifurcating trees and aligns the table columns with the tree tip names
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58
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59
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60 |
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61
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62 </help>
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63 <citations>
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64 <citation type="bibtex">@article{cite1,
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65 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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66 journal = {MSystems},
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67 number = {1},
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68 pages = {e00162--16},
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69 publisher = {Am Soc Microbiol},
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70 title = {Balance trees reveal microbial niche differentiation},
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71 volume = {2},
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72 year = {2017}
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73 }
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74 </citation>
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75 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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76 </citations>
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77 </tool>