Mercurial > repos > q2d2 > qiime2__demux__filter_samples

annotate qiime2__demux__filter_samples.xml @ 2:0e5d4dc5c23e draft

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author q2d2
date Thu, 08 Jun 2023 19:35:58 +0000
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children a23769ef6bd8
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, 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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Filter samples out of demultiplexed data.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version demux</version_command>
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19 <command detect_errors="exit_code">q2galaxy run demux filter_samples '$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="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required] The demultiplexed data from which samples should be filtered.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
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27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
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28 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
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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 ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
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31 </param>
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32 <repeat name="metadata" min="1" help="[required] Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata">
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33 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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34 <param name="type" type="select" label="metadata: Metadata">
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35 <option value="tsv" selected="true">Metadata from TSV</option>
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36 <option value="qza">Metadata from Artifact</option>
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37 </param>
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38 <when value="tsv">
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39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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40 </when>
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41 <when value="qza">
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42 <param name="source" type="data" format="qza" label="Metadata Source"/>
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43 </when>
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44 </conditional>
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45 </repeat>
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46 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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47 <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
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48 <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained.">
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49 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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50 <option value="__q2galaxy__::control::provide">Provide a value</option>
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51 </param>
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52 <when value="__q2galaxy__::control::default">
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53 <param name="where" type="hidden" value="__q2galaxy__::literal::None"/>
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54 </when>
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55 <when value="__q2galaxy__::control::provide">
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56 <param name="where" type="text">
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57 <sanitizer>
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58 <valid initial="string.printable"/>
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59 </sanitizer>
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60 </param>
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61 </when>
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62 </conditional>
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63 <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data."/>
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64 </section>
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65 </inputs>
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66 <outputs>
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67 <data name="filtered_demux" format="qza" label="${tool.name} on ${on_string}: filtered_demux.qza" from_work_dir="filtered_demux.qza"/>
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68 </outputs>
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69 <tests/>
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70 <help>
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71 QIIME 2: demux filter-samples
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72 =============================
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73 Filter samples out of demultiplexed data.
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74
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75
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76 Outputs:
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77 --------
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78 :filtered_demux.qza: Filtered demultiplexed data.
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80 |
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82 Description:
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83 ------------
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84 Filter samples indicated in given metadata out of demultiplexed data. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified.
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87 |
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89 </help>
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90 <citations>
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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>