comparison qiime2__composition__ancombc.xml @ 1:fe99db171ce5 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556

0:9b2a68d3017f

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Analysis of Composition of Microbiomes with Bias Correction</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version composition</version_command>
    <command detect_errors="exit_code">q2galaxy run composition ancombc '$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 to be used for ANCOM computation.">
            <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>

                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="formula" value="bodysite + month"/>
            <repeat name="reference_levels">
                <param name="element" value="bodysite::tongue"/>
            </repeat>
            <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/>

|  

Description:
------------
ANCOM-BC description goes here.

Examples:
---------

ancombc_single_formula

      #. Leave as ``Metadata from TSV``
      #. Set *"Metadata Source"* to ``metadata.tsv``


 #. Set *"formula"* to ``bodysite + month``
 #. Expand the ``additional options`` section

    - For *"reference_levels"*:

      #. Set *"element"* to ``bodysite::tongue``
      #. (Do not insert additional values.)


 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:

|  

</help>
    <citations>
        <citation type="doi">10.3402/mehd.v26.27663</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>

1:fe99db171ce5

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2023.5.0)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Analysis of Composition of Microbiomes with Bias Correction</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version composition</version_command>
    <command detect_errors="exit_code">q2galaxy run composition ancombc '$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 to be used for ANCOM-BC computation.">
            <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>

                <conditional name="__q2galaxy__GUI__conditional__metadata__">
                    <param name="type" value="tsv"/>
                    <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/>
                </conditional>
            </repeat>
            <param name="formula" value="bodysite + animal"/>
            <repeat name="reference_levels">
                <param name="element" value="bodysite::tongue"/>
            </repeat>
            <repeat name="reference_levels">
                <param name="element" value="animal::dog"/>
            </repeat>
            <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/>

|  

Description:
------------
Apply Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) to identify features that are differentially abundant across groups.

Examples:
---------

ancombc_single_formula

      #. Leave as ``Metadata from TSV``
      #. Set *"Metadata Source"* to ``metadata.tsv``


 #. Set *"formula"* to ``bodysite + animal``
 #. Expand the ``additional options`` section

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

      #. Add *"element"* set to ``bodysite::tongue``
      #. Add *"element"* set to ``animal::dog``


 #. Press the ``Execute`` button.

Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:

|  

</help>
    <citations>
        <citation type="doi">10.1038/s41467-020-17041-7</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>