Mercurial > repos > q2d2 > qiime2__diversity__filter_distance_matrix

annotate qiime2__diversity__filter_distance_matrix.xml @ 0:3e9db2758fd2 draft

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author q2d2
date Mon, 29 Aug 2022 19:38:17 +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) 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 diversity filter-distance-matrix" id="qiime2__diversity__filter_distance_matrix" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Filter samples from a distance matrix.</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 diversity</version_command>
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19 <command detect_errors="aggressive">q2galaxy run diversity filter_distance_matrix '$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="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] Distance matrix to filter by sample.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="DistanceMatrix"/>
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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 ['DistanceMatrix']</validator>
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29 </param>
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30 <repeat name="metadata" min="1" help="[required] Sample metadata used with `where` parameter when selecting samples to retain, or with `exclude_ids` when selecting samples to discard." title="metadata: Metadata">
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31 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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32 <param name="type" type="select" label="metadata: Metadata">
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33 <option value="tsv" selected="true">Metadata from TSV</option>
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34 <option value="qza">Metadata from Artifact</option>
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35 </param>
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36 <when value="tsv">
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37 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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38 </when>
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39 <when value="qza">
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40 <param name="source" type="data" format="qza" label="Metadata Source"/>
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41 </when>
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42 </conditional>
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43 </repeat>
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44 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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45 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
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46 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered distance matrix. If not provided, all samples in `metadata` that are also in the input distance matrix will be retained.">
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47 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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48 <option value="__q2galaxy__::control::provide">Provide a value</option>
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49 </param>
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50 <when value="__q2galaxy__::control::default">
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51 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/>
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52 </when>
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53 <when value="__q2galaxy__::control::provide">
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54 <param name="where" type="text">
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55 <sanitizer>
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56 <valid initial="string.printable"/>
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57 </sanitizer>
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58 </param>
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59 </when>
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60 </conditional>
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61 <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] If `True`, the samples selected by `metadata` or `where` parameters will be excluded from the filtered distance matrix instead of being retained."/>
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62 </section>
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63 </inputs>
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64 <outputs>
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65 <data name="filtered_distance_matrix" format="qza" label="${tool.name} on ${on_string}: filtered_distance_matrix.qza" from_work_dir="filtered_distance_matrix.qza"/>
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66 </outputs>
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67 <tests/>
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68 <help>
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69 QIIME 2: diversity filter-distance-matrix
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70 =========================================
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71 Filter samples from a distance matrix.
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72
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73
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74 Outputs:
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75 --------
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76 :filtered_distance_matrix.qza: Distance matrix filtered to include samples matching search criteria
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77
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78 |
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80 Description:
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81 ------------
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82 Filter samples from a distance matrix, retaining only the samples matching search criteria specified by `metadata` and `where` parameters (or retaining only the samples not matching that criteria, if `exclude_ids` is True). See the filtering tutorial on https://docs.qiime2.org for additional details.
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85 |
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87 </help>
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88 <citations>
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89 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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90 </citations>
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91 </tool>