annotate qiime2__diversity_lib__observed_features.xml @ 8:19e3205e8206 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.10.0)
for:
    qiime2 (version: 2025.10.0)
-->
<tool name="qiime2 diversity-lib observed-features" id="qiime2__diversity_lib__observed_features" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Observed Features</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
    </requirements>
    <version_command>q2galaxy version diversity_lib</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity_lib observed_features '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="observed_features.test0.feature-table.qza" ftype="qza"/>
            <output name="vector" ftype="qza">
                <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: SampleData\[AlphaDiversity\]"/>
                    </has_archive_member>
                    <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}\/data\/alpha-diversity.tsv">
                        <has_line_matching expression="S1&#9;1"/>
                        <has_line_matching expression="S2&#9;1"/>
                        <has_line_matching expression="S3&#9;2"/>
                        <has_line_matching expression="S4&#9;2"/>
                        <has_line_matching expression="S5&#9;3"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: diversity-lib observed-features
========================================
Observed Features


Outputs:
--------
:vector.qza: Vector containing per-sample counts of observed features.

|  

Description:
------------
Compute the number of observed features for each sample in a feature table

Examples:
---------

basic
*****
Using the ``qiime2 diversity-lib observed-features`` tool:
 #. Set *"table"* to ``#: feature-table.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 diversity-lib observed-features [...] : vector.qza``
      - ``obs-feat-vector.qza``


|  

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