annotate qiime2__diversity_lib__bray_curtis.xml @ 0:7330b10c19a7 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 bray-curtis" id="qiime2__diversity_lib__bray_curtis" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Bray-Curtis Dissimilarity</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 bray_curtis '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table containing the samples for which Bray-Curtis dissimilarity should be computed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
                <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched 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="n_jobs" type="hidden" value="auto"/>
                </when>
                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
                    <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
                </when>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="table" value="bray_curtis.test0.feature-table.qza" ftype="qza"/>
            <output name="distance_matrix" 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: DistanceMatrix"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="table" value="bray_curtis.test1.feature-table.qza" ftype="qza"/>
            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
                <param name="n_jobs" value="1"/>
            </conditional>
            <output name="distance_matrix" 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: DistanceMatrix"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="table" value="bray_curtis.test2.feature-table.qza" ftype="qza"/>
            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
                <param name="__q2galaxy__GUI__select__" value="auto"/>
                <param name="n_jobs" value="auto"/>
            </conditional>
            <output name="distance_matrix" 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: DistanceMatrix"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: diversity-lib bray-curtis
==================================
Bray-Curtis Dissimilarity


Outputs:
--------
:distance_matrix.qza: Distance matrix for Bray-Curtis dissimilarity

|  

Description:
------------
Compute Bray-Curtis dissimilarity for each sample in a feature table. Note: Frequency and relative frequency data produce different results unless overall sample sizes are identical. Please consider the impact on your results if you use Bray-Curtis with count data that has not been adjusted (normalized).

Examples:
---------

run on one core (by default)
****************************
Using the ``qiime2 diversity-lib bray-curtis`` 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 bray-curtis [...] : distance_matrix.qza``
      - ``bray-curtis-dm.qza``

to run on n cores, replace 1 here with your preferred integer
*************************************************************
Using the ``qiime2 diversity-lib bray-curtis`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Expand the ``additional options`` section

    - Leave *"n_jobs"* as its default value of ``1``

 #. 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 bray-curtis [...] : distance_matrix.qza``
      - ``bray-curtis-dm.qza``

use 'auto' to run on all of host system's available CPU cores
*************************************************************
Using the ``qiime2 diversity-lib bray-curtis`` tool:
 #. Set *"table"* to ``#: feature-table.qza``
 #. Expand the ``additional options`` section

    - Set *"n_jobs"* to ``auto``

 #. 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 bray-curtis [...] : distance_matrix.qza``
      - ``bray-curtis-dm.qza``


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Sørensen, Thorvald},
 journal = {Biol. Skr.},
 pages = {1--34},
 title = {A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on Danish commons},
 volume = {5},
 year = {1948}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>