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annotate qiime2__longitudinal__first_distances.xml @ 3:54f724ba9dc6 draft

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author q2d2
date Thu, 25 Apr 2024 21:15:43 +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: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 longitudinal first-distances" id="qiime2__longitudinal__first_distances" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Compute first distances or distance from baseline between sequential states</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
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17 </requirements>
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18 <version_command>q2galaxy version longitudinal</version_command>
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19 <command detect_errors="exit_code">q2galaxy run longitudinal first_distances '$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="distance_matrix" type="data" format="qza" label="distance_matrix: DistanceMatrix" help="[required] Matrix of distances between pairs of samples.">
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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 file containing individual_id_column." 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 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information.">
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45 <sanitizer>
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46 <valid initial="string.printable"/>
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47 </sanitizer>
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48 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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49 </param>
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50 <param name="individual_id_column" type="text" label="individual_id_column: Str" help="[required] Metadata column containing IDs for individual subjects.">
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51 <sanitizer>
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52 <valid initial="string.printable"/>
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53 </sanitizer>
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54 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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55 </param>
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56 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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57 <param name="baseline" type="float" optional="true" label="baseline: Float" help="[optional] A value listed in the state_column metadata column against which all other states should be compared. Toggles calculation of static distances instead of first distances (which are calculated if no value is given for baseline). If a &quot;baseline&quot; value is provided, sample distances at each state are compared against the baseline state, instead of the previous state. Must be a value listed in the state_column."/>
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58 <param name="replicate_handling" type="select" label="replicate_handling: Str % Choices('error', 'random', 'drop')" display="radio">
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59 <option value="error" selected="true">error</option>
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60 <option value="random">random</option>
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61 <option value="drop">drop</option>
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62 </param>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data name="first_distances" format="qza" label="${tool.name} on ${on_string}: first_distances.qza" from_work_dir="first_distances.qza"/>
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67 </outputs>
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68 <tests/>
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69 <help>
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70 QIIME 2: longitudinal first-distances
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71 =====================================
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72 Compute first distances or distance from baseline between sequential states
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73
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74
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75 Outputs:
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76 --------
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77 :first_distances.qza: Series of first distances.
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78
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81 Description:
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82 ------------
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83 Calculates first distances between sequential states for samples collected from individual subjects sampled repeatedly at two or more states. This method is similar to the "first differences" method, except that it requires a distance matrix as input and calculates first differences as distances between successive states. Outputs a data series of first distances for each individual subject at each sequential pair of states, labeled by the SampleID of the second state (e.g., paired distances between time 0 and time 1 would be labeled by the SampleIDs at time 1). This file can be used as input to linear mixed effects models or other longitudinal or diversity methods to compare changes in first distances across time or among groups of subjects. Also supports distance from baseline (or other static comparison state) by setting the "baseline" parameter.
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88 </help>
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89 <citations>
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90 <citation type="doi">10.1128/mSystems.00219-18</citation>
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91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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92 </citations>
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93 </tool>