annotate qiime2__diversity_lib__faith_pd.xml @ 0:787fb9ea6f43 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 diversity-lib faith-pd" id="qiime2__diversity_lib__faith_pd" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Faith's Phylogenetic Diversity</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version diversity_lib</version_command>
    <command detect_errors="aggressive">q2galaxy run diversity_lib faith_pd '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </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[Frequency]"/>
                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
                <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>
        <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>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__threads__">
                <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host.">
                    <option value="auto">auto (Str)</option>
                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
                </param>
                <when value="auto">
                    <param name="threads" type="hidden" value="auto"/>
                </when>
                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
                    <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/>
                </when>
            </conditional>
        </section>
    </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>