annotate qiime2__diversity_lib__faith_pd.xml @ 3:c2eccef98006 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 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 diversity-lib faith-pd" id="qiime2__diversity_lib__faith_pd" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Faith's Phylogenetic Diversity</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version diversity_lib</version_command>
    <command detect_errors="exit_code">q2galaxy run diversity_lib faith_pd '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which Faith's phylogenetic diversity should be computed. Table values will be converted to presence/absence.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
        </param>
        <param name="phylogeny" type="data" format="qza" label="phylogeny: Phylogeny[Rooted]" help="[required]  Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="faith_pd.test0.feature-table.qza" ftype="qza"/>
            <param name="phylogeny" value="faith_pd.test0.phylogeny.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>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: diversity-lib faith-pd
===============================
Faith's Phylogenetic Diversity


Outputs:
--------
:vector.qza: Vector containing per-sample values for Faith's Phylogenetic Diversity.

|  

Description:
------------
Computes Faith's Phylogenetic Diversity for all samples in a feature table.

Examples:
---------

basic
*****
Using the ``qiime2 diversity-lib faith-pd`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Set *"phylogeny"* to ``#: phylogeny.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 faith-pd [...] : vector.qza``
      - ``faith-pd-vector.qza``


|  

</help>
    <citations>
        <citation type="doi">10.1016/0006-3207(92)91201-3</citation>
        <citation type="doi">10.1101/gr.275777.121</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>