annotate qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml @ 0:e1dbc6a12aa9 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 beta-phylogenetic-meta-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_meta_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Beta Phylogenetic Meta Passthrough</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 beta_phylogenetic_meta_passthrough '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]]" help="[required]  The feature tables containing the samples over which beta diversity should be computed." multiple="true">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
        </param>
        <param name="phylogenies" type="data" format="qza" label="phylogenies: List[Phylogeny[Rooted]]" help="[required]  Phylogenetic trees 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." multiple="true">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
        </param>
        <param name="metric" type="select" label="metric: Str % Choices('generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac')" display="radio">
            <option value="__q2galaxy__::literal::None">Selection required</option>
            <option value="generalized_unifrac">generalized_unifrac</option>
            <option value="unweighted_unifrac">unweighted_unifrac</option>
            <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
            <option value="weighted_unifrac">weighted_unifrac</option>
            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</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>
            <param name="variance_adjusted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="variance_adjusted: Bool" help="[default: No]  Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation."/>
            <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional]  This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized."/>
            <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No]  In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/>
            <repeat name="weights" help="[optional]  The weight applied to each tree/table pair. This tuple is expected to be in index order with tables and phylogenies. Default is to weight each tree/table pair evenly." title="weights: List[Float]">
                <param name="element" type="float" value="" label="element: Float" help="[required]"/>
            </repeat>
            <param name="consolidation" type="select" label="consolidation: Str % Choices('skipping_missing_matrices', 'missing_zero', 'missing_one', 'skipping_missing_values')" display="radio">
                <option value="skipping_missing_matrices">skipping_missing_matrices</option>
                <option value="missing_zero">missing_zero</option>
                <option value="missing_one">missing_one</option>
                <option value="skipping_missing_values" selected="true">skipping_missing_values</option>
            </param>
        </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="tables" value="beta_phylogenetic_meta_passthrough.test0.feature-table1.qza,beta_phylogenetic_meta_passthrough.test0.feature-table2.qza" ftype="qza"/>
            <param name="phylogenies" value="beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza,beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza" ftype="qza"/>
            <param name="metric" value="weighted_normalized_unifrac"/>
            <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="tables" value="beta_phylogenetic_meta_passthrough.test1.feature-table1.qza,beta_phylogenetic_meta_passthrough.test1.feature-table2.qza" ftype="qza"/>
            <param name="phylogenies" value="beta_phylogenetic_meta_passthrough.test1.phylogeny.qza,beta_phylogenetic_meta_passthrough.test1.phylogeny.qza" ftype="qza"/>
            <param name="metric" value="weighted_normalized_unifrac"/>
            <repeat name="weights">
                <param name="element" value="3.0"/>
            </repeat>
            <repeat name="weights">
                <param name="element" value="42.0"/>
            </repeat>
            <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="tables" value="beta_phylogenetic_meta_passthrough.test2.feature-table1.qza,beta_phylogenetic_meta_passthrough.test2.feature-table2.qza" ftype="qza"/>
            <param name="phylogenies" value="beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza,beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza" ftype="qza"/>
            <param name="metric" value="weighted_normalized_unifrac"/>
            <repeat name="weights">
                <param name="element" value="0.4"/>
            </repeat>
            <repeat name="weights">
                <param name="element" value="0.6"/>
            </repeat>
            <param name="consolidation" value="skipping_missing_values"/>
            <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 beta-phylogenetic-meta-passthrough
=========================================================
Beta Phylogenetic Meta Passthrough


Outputs:
--------
:distance_matrix.qza: The resulting distance matrix.

|  

Description:
------------
Computes a distance matrix for all pairs of samples in the set of feature table and phylogeny pairs, using the unifrac implementation of the selected beta diversity metric.

Examples:
---------

Basic meta unifrac
******************
| For brevity, these examples are focused on meta-specific parameters. See the documentation for beta_phylogenetic_passthrough for additional relevant information.
| NOTE: the number of trees and tables must match.
Using the ``qiime2 diversity-lib beta-phylogenetic-meta-passthrough`` tool:
 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: feature-table1.qza``
    #. ``#: feature-table2.qza``

 #. For *"phylogenies"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: phylogeny1.qza``
    #. ``#: phylogeny2.qza``

 #. Set *"metric"* to ``weighted_normalized_unifrac``
 #. 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 beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza``
      - ``ft1-ft2-w-norm-unifrac-dm.qza``

meta with weights
*****************
| The number of weights must match the number of tables/trees.
| If meaningful, it is possible to pass the same phylogeny more than once.
Using the ``qiime2 diversity-lib beta-phylogenetic-meta-passthrough`` tool:
 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: feature-table1.qza``
    #. ``#: feature-table2.qza``

 #. For *"phylogenies"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: phylogeny.qza``
    #. ``#: phylogeny.qza``

 #. Set *"metric"* to ``weighted_normalized_unifrac``
 #. Expand the ``additional options`` section

    - For *"weights"*, use the ``+ weights`` button to add the corresponding values:

      #. Add *"element"* set to ``3.0``
      #. Add *"element"* set to ``42.0``


 #. 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 beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza``
      - ``ft1-ft2-w-norm-unifrac-dm.qza``

changing the consolidation method
*********************************
Using the ``qiime2 diversity-lib beta-phylogenetic-meta-passthrough`` tool:
 #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: feature-table1.qza``
    #. ``#: feature-table2.qza``

 #. For *"phylogenies"*, use ctrl-(or command)-click to select the following inputs:

    #. ``#: phylogeny1.qza``
    #. ``#: phylogeny2.qza``

 #. Set *"metric"* to ``weighted_normalized_unifrac``
 #. Expand the ``additional options`` section

    #. For *"weights"*, use the ``+ weights`` button to add the corresponding values:

       #. Add *"element"* set to ``0.4``
       #. Add *"element"* set to ``0.6``

    #. Leave *"consolidation"* as its default value of ``skipping_missing_values``

 #. 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 beta-phylogenetic-meta-passthrough [...] : distance_matrix.qza``
      - ``ft1-ft2-w-norm-unifrac-dm.qza``


|  

</help>
    <citations>
        <citation type="doi">10.1128/AEM.71.12.8228-8235.2005</citation>
        <citation type="doi">10.1128/AEM.01996-06</citation>
        <citation type="doi">10.1038/ismej.2009.97</citation>
        <citation type="doi">10.1038/ismej.2010.133</citation>
        <citation type="doi">10.1038/s41592-018-0187-8</citation>
        <citation type="doi">10.1186/1471-2105-12-118</citation>
        <citation type="doi">10.1093/bioinformatics/bts342</citation>
        <citation type="doi">10.1073/pnas.0807339105</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>