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author q2d2
date Mon, 05 May 2025 18:50:28 +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) 2025, 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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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2025.4.0)
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10 for:
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11 qiime2 (version: 2025.4.0)
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12 -->
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13 <tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
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14 <description>View sequence associated with each feature</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:2025.4</container>
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20 </requirements>
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21 <version_command>q2galaxy version feature_table</version_command>
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22 <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$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="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Sequence]"/>
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30 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
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31 </options>
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32 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
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33 </param>
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34 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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35 <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: Collection[FeatureData[Taxonomy]]" help="[optional] The taxonomic classifications of the tabulated features." multiple="true">
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36 <options options_filter_attribute="metadata.semantic_type">
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37 <filter type="add_value" value="FeatureData[Taxonomy]"/>
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38 </options>
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39 </param>
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40 <repeat name="metadata" help="[optional] Any additional metadata for the tabulated features." title="metadata: Metadata">
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41 <conditional name="__q2galaxy__GUI__conditional__metadata__">
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42 <param name="type" type="select" label="metadata: Metadata">
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43 <option value="tsv" selected="true">Metadata from TSV</option>
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44 <option value="qza">Metadata from Artifact</option>
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45 </param>
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46 <when value="tsv">
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47 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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48 </when>
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49 <when value="qza">
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50 <param name="source" type="data" format="qza" label="Metadata Source"/>
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51 </when>
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52 </conditional>
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53 </repeat>
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54 <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio">
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55 <option value="strict" selected="true">strict</option>
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56 <option value="union">union</option>
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57 <option value="intersect">intersect</option>
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58 </param>
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59 </section>
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60 </inputs>
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61 <outputs>
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62 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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63 </outputs>
1
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64 <tests>
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65 <test>
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66 <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/>
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67 <output name="visualization" ftype="qzv">
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68 <assert_contents>
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69 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
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70 <has_line_matching expression="type: Visualization"/>
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71 </has_archive_member>
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72 </assert_contents>
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73 </output>
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74 </test>
3
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75 <test>
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76 <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/>
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77 <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/>
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78 <output name="visualization" ftype="qzv">
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79 <assert_contents>
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80 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
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81 <has_line_matching expression="type: Visualization"/>
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82 </has_archive_member>
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83 </assert_contents>
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84 </output>
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85 </test>
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86 <test>
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87 <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/>
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88 <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/>
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89 <output name="visualization" ftype="qzv">
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90 <assert_contents>
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91 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
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92 <has_line_matching expression="type: Visualization"/>
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93 </has_archive_member>
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94 </assert_contents>
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95 </output>
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96 </test>
1
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97 </tests>
0
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98 <help>
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99 QIIME 2: feature-table tabulate-seqs
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100 ====================================
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101 View sequence associated with each feature
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102
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103
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104 Outputs:
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105 --------
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106 :visualization.qzv: &lt;no description&gt;
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107
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108 |
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109
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110 Description:
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111 ------------
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112 Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.
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113
1
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114 Examples:
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115 ---------
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116
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117 feature_table_tabulate_seqs
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118 ***************************
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119 Using the ``qiime2 feature-table tabulate-seqs`` tool:
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120 #. Set *"data"* to ``#: rep-seqs.qza``
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121 #. Press the ``Execute`` button.
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122
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123 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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124 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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125
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126 .. list-table::
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127 :align: left
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128 :header-rows: 1
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129
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130 * - History Name
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131 - *"Name"* to set (be sure to press ``Save``)
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132 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
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133 - ``rep-seqs.qzv``
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134
3
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135 feature_table_tabulate_seqs_single_taxon
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136 ****************************************
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137 Using the ``qiime2 feature-table tabulate-seqs`` tool:
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138 #. Set *"data"* to ``#: rep-seqs-single-taxon.qza``
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139 #. Expand the ``additional options`` section
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140
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141 - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']``
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142
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143 #. Press the ``Execute`` button.
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144
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145 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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146 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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147
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148 .. list-table::
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149 :align: left
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150 :header-rows: 1
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151
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152 * - History Name
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153 - *"Name"* to set (be sure to press ``Save``)
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154 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
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155 - ``rep-seqs.qzv``
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156
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157 feature_table_tabulate_seqs_multi_taxon
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158 ***************************************
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159 Using the ``qiime2 feature-table tabulate-seqs`` tool:
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160 #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza``
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161 #. Expand the ``additional options`` section
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162
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163 - Set *"taxonomy"* to ``#: multi-taxonomy/``
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164
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165 #. Press the ``Execute`` button.
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166
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167 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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168 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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169
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170 .. list-table::
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171 :align: left
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172 :header-rows: 1
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173
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174 * - History Name
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175 - *"Name"* to set (be sure to press ``Save``)
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176 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
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177 - ``rep-seqs.qzv``
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178
0
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179
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180 |
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181
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182 </help>
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183 <citations>
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184 <citation type="doi">10.1093/nar/gkw1071</citation>
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185 <citation type="doi">10.1093/nar/gkn201</citation>
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186 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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187 </citations>
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188 </tool>