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author q2d2
date Mon, 03 Jun 2024 23:29:55 +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) 2024, 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: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 phylogeny filter-table" id="qiime2__phylogeny__filter_table" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Remove features from table if they're not present in tree.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version phylogeny</version_command>
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19 <command detect_errors="exit_code">q2galaxy run phylogeny filter_table '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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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[Frequency¹ | RelativeFrequency² | PresenceAbsence³]" help="[required] Feature table that features should be filtered from.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
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27 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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28 <filter type="add_value" value="FeatureTable[Frequency]"/>
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29 </options>
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30 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
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31 </param>
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32 <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted | Unrooted]" help="[required] Tree where tip identifiers are the feature identifiers that should be retained in the table.">
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33 <options options_filter_attribute="metadata.semantic_type">
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34 <filter type="add_value" value="Phylogeny[Rooted]"/>
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35 <filter type="add_value" value="Phylogeny[Unrooted]"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']</validator>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
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42 </outputs>
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43 <tests/>
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44 <help>
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45 QIIME 2: phylogeny filter-table
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46 ===============================
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47 Remove features from table if they're not present in tree.
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48
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49
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50 Outputs:
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51 --------
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52 :filtered_table.qza: The resulting feature table.
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54 |
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56 Description:
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57 ------------
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58 Remove features from a feature table if their identifiers are not tip identifiers in tree.
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59
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61 |
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63 </help>
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64 <citations>
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65 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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66 </citations>
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67 </tool>