Mercurial > repos > q2d2 > qiime2__longitudinal__first_differences
annotate qiime2__longitudinal__first_differences.xml @ 0:8913c08bc41d draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:07:49 +0000 |
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children | 372affefd8a3 |
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8913c08bc41d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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3 Copyright (c) 2022, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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9 q2galaxy (version: 2022.8.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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11 qiime2 (version: 2022.8.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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13 <tool name="qiime2 longitudinal first-differences" id="qiime2__longitudinal__first_differences" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Compute first differences or difference from baseline between sequential states</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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16 <container type="docker">quay.io/qiime2/core:2022.8</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version longitudinal</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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19 <command detect_errors="aggressive">q2galaxy run longitudinal first_differences '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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21 <inputs name="inputs" data_style="paths"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <param name="type" type="select" label="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <option value="tsv" selected="true">Metadata from TSV</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <option value="qza">Metadata from Artifact</option> |
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29 </param> |
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30 <when value="tsv"> |
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31 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 </when> |
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33 <when value="qza"> |
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34 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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35 </when> |
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36 </conditional> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 </repeat> |
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38 <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information."> |
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39 <sanitizer> |
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40 <valid initial="string.printable"/> |
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41 </sanitizer> |
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42 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> |
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43 </param> |
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44 <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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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) > 0</validator> |
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49 </param> |
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50 <param name="metric" type="text" label="metric: Str" help="[required] Numerical metadata or artifact column to test."> |
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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) > 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="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table to optionally use for computing first differences."> |
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58 <options options_filter_attribute="metadata.semantic_type"> |
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59 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
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60 </options> |
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61 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[RelativeFrequency]']</validator> |
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62 </param> |
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63 <param name="replicate_handling" type="select" label="replicate_handling: Str % Choices('error', 'random', 'drop')" display="radio"> |
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64 <option value="error" selected="true">error</option> |
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65 <option value="random">random</option> |
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66 <option value="drop">drop</option> |
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67 </param> |
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68 <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 differences instead of first differences (which are calculated if no value is given for baseline). If a "baseline" value is provided, sample differences 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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69 </section> |
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70 </inputs> |
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71 <outputs> |
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72 <data name="first_differences" format="qza" label="${tool.name} on ${on_string}: first_differences.qza" from_work_dir="first_differences.qza"/> |
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73 </outputs> |
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74 <tests/> |
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75 <help> |
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76 QIIME 2: longitudinal first-differences |
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77 ======================================= |
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78 Compute first differences or difference from baseline between sequential states |
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79 |
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80 |
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81 Outputs: |
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82 -------- |
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83 :first_differences.qza: Series of first differences. |
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84 |
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85 | |
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86 |
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87 Description: |
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88 ------------ |
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89 Calculates first differences in "metric" between sequential states for samples collected from individual subjects sampled repeatedly at two or more states. First differences can be performed on a metadata column (including artifacts that can be input as metadata) or a feature in a feature table. Outputs a data series of first differences for each individual subject at each sequential pair of states, labeled by the SampleID of the second state (e.g., paired differences 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 differences across time or among groups of subjects. Also supports differences from baseline (or other static comparison state) by setting the "baseline" parameter. |
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90 |
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91 |
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92 | |
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93 |
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94 </help> |
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95 <citations> |
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96 <citation type="doi">10.1128/mSystems.00219-18</citation> |
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97 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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98 </citations> |
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99 </tool> |