Mercurial > repos > q2d2 > qiime2__quality_control__decontam_identify

annotate qiime2__quality_control__decontam_identify.xml @ 3:653d55f191df draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:54:18 +0000
parents 99bf4ed8cb61
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ba52336465f9 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
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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: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 quality-control decontam-identify" id="qiime2__quality_control__decontam_identify" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Identify contaminants</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version quality_control</version_command>
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22 <command detect_errors="exit_code">q2galaxy run quality_control decontam_identify '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table which contaminate sequences will be identified from">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
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32 </param>
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33 <repeat name="metadata" min="1" help="[required] metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter" title="metadata: Metadata">
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34 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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35 <param name="type" type="select" label="metadata: Metadata">
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36 <option value="tsv" selected="true">Metadata from TSV</option>
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37 <option value="qza">Metadata from Artifact</option>
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38 </param>
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39 <when value="tsv">
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40 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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41 </when>
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42 <when value="qza">
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43 <param name="source" type="data" format="qza" label="Metadata Source"/>
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44 </when>
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45 </conditional>
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46 </repeat>
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47 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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48 <param name="method" type="select" label="method: Str % Choices('combined', 'frequency', 'prevalence')" display="radio">
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49 <option value="combined">combined</option>
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50 <option value="frequency">frequency</option>
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51 <option value="prevalence" selected="true">prevalence</option>
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52 </param>
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53 <conditional name="__q2galaxy__GUI__conditional__freq_concentration_column__" label="freq_concentration_column: Str">
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54 <param name="__q2galaxy__GUI__select__" type="select" label="freq_concentration_column: Str" help="[optional] Input column name that has concentration information for the samples">
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55 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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56 <option value="__q2galaxy__::control::provide">Provide a value</option>
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57 </param>
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58 <when value="__q2galaxy__::control::default">
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59 <param name="freq_concentration_column" type="hidden" value="__q2galaxy__::literal::None"/>
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60 </when>
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61 <when value="__q2galaxy__::control::provide">
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62 <param name="freq_concentration_column" type="text">
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63 <sanitizer>
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64 <valid initial="string.printable"/>
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65 </sanitizer>
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66 </param>
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67 </when>
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68 </conditional>
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69 <conditional name="__q2galaxy__GUI__conditional__prev_control_column__" label="prev_control_column: Str">
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70 <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_column: Str" help="[optional] Input column name containing experimental or control sample metadata">
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71 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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72 <option value="__q2galaxy__::control::provide">Provide a value</option>
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73 </param>
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74 <when value="__q2galaxy__::control::default">
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75 <param name="prev_control_column" type="hidden" value="__q2galaxy__::literal::None"/>
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76 </when>
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77 <when value="__q2galaxy__::control::provide">
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78 <param name="prev_control_column" type="text">
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79 <sanitizer>
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80 <valid initial="string.printable"/>
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81 </sanitizer>
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82 </param>
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83 </when>
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84 </conditional>
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85 <conditional name="__q2galaxy__GUI__conditional__prev_control_indicator__" label="prev_control_indicator: Str">
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86 <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_indicator: Str" help="[optional] indicate the control sample identifier (e.g. &quot;control&quot; or &quot;blank&quot;)">
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87 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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88 <option value="__q2galaxy__::control::provide">Provide a value</option>
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89 </param>
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90 <when value="__q2galaxy__::control::default">
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91 <param name="prev_control_indicator" type="hidden" value="__q2galaxy__::literal::None"/>
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92 </when>
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93 <when value="__q2galaxy__::control::provide">
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94 <param name="prev_control_indicator" type="text">
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95 <sanitizer>
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96 <valid initial="string.printable"/>
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97 </sanitizer>
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98 </param>
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99 </when>
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100 </conditional>
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101 </section>
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102 </inputs>
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103 <outputs>
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104 <data name="decontam_scores" format="qza" label="${tool.name} on ${on_string}: decontam_scores.qza" from_work_dir="decontam_scores.qza"/>
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105 </outputs>
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106 <tests/>
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107 <help>
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108 QIIME 2: quality-control decontam-identify
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109 ==========================================
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110 Identify contaminants
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111
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112
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113 Outputs:
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114 --------
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115 :decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence
0
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116
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117 |
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118
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119 Description:
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120 ------------
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121 This method identifies contaminant sequences from an OTU or ASV table and reports them to the user
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122
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123
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124 |
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125
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126 </help>
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127 <citations>
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128 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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129 </citations>
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130 </tool>