view qiime2__feature_table__tabulate_seqs.xml @ 3:2feea4c63f4c draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2024, QIIME 2 development team.

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>View sequence associated with each feature</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version feature_table</version_command>
    <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required]  The feature sequences to be tabulated.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <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">
                <options options_filter_attribute="metadata.semantic_type">
                    <filter type="add_value" value="FeatureData[Taxonomy]"/>
                </options>
            </param>
            <repeat name="metadata" help="[optional]  Any additional metadata for the tabulated features." title="metadata: Metadata">
                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" type="select" label="metadata: Metadata">
                        <option value="tsv" selected="true">Metadata from TSV</option>
                        <option value="qza">Metadata from Artifact</option>
                    </param>
                    <when value="tsv">
                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                    </when>
                    <when value="qza">
                        <param name="source" type="data" format="qza" label="Metadata Source"/>
                    </when>
                </conditional>
            </repeat>
            <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio">
                <option value="strict" selected="true">strict</option>
                <option value="union">union</option>
                <option value="intersect">intersect</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests>
        <test>
            <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/>
            <output name="visualization" ftype="qzv">
                <assert_contents>
                    <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">
                        <has_line_matching expression="type: Visualization"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/>
            <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/>
            <output name="visualization" ftype="qzv">
                <assert_contents>
                    <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">
                        <has_line_matching expression="type: Visualization"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/>
            <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/>
            <output name="visualization" ftype="qzv">
                <assert_contents>
                    <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">
                        <has_line_matching expression="type: Visualization"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: feature-table tabulate-seqs
====================================
View sequence associated with each feature


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.

Examples:
---------

feature_table_tabulate_seqs
***************************
Using the ``qiime2 feature-table tabulate-seqs`` tool:
 #. Set *"data"* to ``#: rep-seqs.qza``
 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
      - ``rep-seqs.qzv``

feature_table_tabulate_seqs_single_taxon
****************************************
Using the ``qiime2 feature-table tabulate-seqs`` tool:
 #. Set *"data"* to ``#: rep-seqs-single-taxon.qza``
 #. Expand the ``additional options`` section

    - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']``

 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
      - ``rep-seqs.qzv``

feature_table_tabulate_seqs_multi_taxon
***************************************
Using the ``qiime2 feature-table tabulate-seqs`` tool:
 #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza``
 #. Expand the ``additional options`` section

    - Set *"taxonomy"* to ``#: multi-taxonomy/``

 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
      - ``rep-seqs.qzv``


|  

</help>
    <citations>
        <citation type="doi">10.1093/nar/gkw1071</citation>
        <citation type="doi">10.1093/nar/gkn201</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>