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annotate qiime2__taxa__collapse.xml @ 0:3e34b8065c52 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:29:53 +0000
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3e34b8065c52 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2022, QIIME 2 development team.
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4
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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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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13 <tool name="qiime2 taxa collapse" id="qiime2__taxa__collapse" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Collapse features by their taxonomy at the specified level</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</container>
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17 </requirements>
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18 <version_command>q2galaxy version taxa</version_command>
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19 <command detect_errors="aggressive">q2galaxy run taxa collapse '$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] Feature table to be collapsed.">
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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="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.">
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31 <options options_filter_attribute="metadata.semantic_type">
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32 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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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 ['FeatureData[Taxonomy]']</validator>
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35 </param>
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36 <param name="level" type="integer" value="" label="level: Int" help="[required] The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation."/>
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37 </inputs>
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38 <outputs>
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39 <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.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: taxa collapse
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44 ======================
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45 Collapse features by their taxonomy at the specified level
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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 :collapsed_table.qza: The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels.
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51
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52 |
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53
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54 Description:
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55 ------------
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56 Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed.
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57
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58
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59 |
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60
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61 </help>
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62 <citations>
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63 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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64 </citations>
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65 </tool>