annotate qiime2__composition__add_pseudocount.xml @ 0:1ba5ca5ccc3e draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 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 composition add-pseudocount" id="qiime2__composition__add_pseudocount" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Add pseudocount to table</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version composition</version_command>
    <command detect_errors="aggressive">q2galaxy run composition add_pseudocount '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to which pseudocounts should be added.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="pseudocount" type="integer" value="1" label="pseudocount: Int" help="[default: 1]  The value to add to all counts in the feature table."/>
        </section>
    </inputs>
    <outputs>
        <data name="composition_table" format="qza" label="${tool.name} on ${on_string}: composition_table.qza" from_work_dir="composition_table.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: composition add-pseudocount
====================================
Add pseudocount to table


Outputs:
--------
:composition_table.qza: The resulting feature table.

|  

Description:
------------
Increment all counts in table by pseudocount.


|  

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