annotate qiime2__diversity_lib__pielou_evenness.xml @ 0:99b04636e7b5 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 pielou-evenness" id="qiime2__diversity_lib__pielou_evenness" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Pielou's Evenness</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 pielou_evenness '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required]  The feature table containing the samples for which Pielou's evenness should be computed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="drop_undefined_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="drop_undefined_samples: Bool" help="[default: No]  Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector."/>
        </section>
    </inputs>
    <outputs>
        <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="pielou_evenness.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>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="table" value="pielou_evenness.test1.feature-table.qza" ftype="qza"/>
            <param name="drop_undefined_samples" value="__q2galaxy__::literal::True"/>
            <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 pielou-evenness
======================================
Pielou's Evenness


Outputs:
--------
:vector.qza: Vector containing per-sample values for Pielou's Evenness.

|  

Description:
------------
Compute Pielou's Evenness for each sample in a feature table

Examples:
---------

basic
*****
Using the ``qiime2 diversity-lib pielou-evenness`` 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 pielou-evenness [...] : vector.qza``
      - ``pielou-vector.qza``

dropping undefined samples
**************************
Using the ``qiime2 diversity-lib pielou-evenness`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Expand the ``additional options`` section

    - Set *"drop_undefined_samples"* to ``Yes``

 #. 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 pielou-evenness [...] : vector.qza``
      - ``pielou-vector.qza``


|  

</help>
    <citations>
        <citation type="doi">10.1016/0022-5193(66)90013-0</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>