view qiime2__rescript__evaluate_seqs.xml @ 1:6ac548ed17c3 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit c7e80dcda727ce63b42aa8a946e9330310929797

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2024, 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: 2024.5.0)
for:
    qiime2 (version: 2024.5.0)
-->
<tool name="qiime2 rescript evaluate-seqs" id="qiime2__rescript__evaluate_seqs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
    <description>Compute summary statistics on sequence artifact(s).</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript evaluate_seqs '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="sequences" type="data" format="qza" label="sequences: List[FeatureData[Sequence]]" help="[required]  One or more sets of sequences to evaluate." multiple="true">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <repeat name="labels" help="[optional]  List of labels to use for labeling evaluation results in the resulting visualization. Inputs are labeled with labels in the order that each is input. If there are fewer labels than inputs (or no labels), unnamed inputs are labeled numerically in sequential order. Extra labels are ignored." title="labels: List[Str]">
                <param name="element" type="text" label="element: Str" help="[required]">
                    <sanitizer>
                        <valid initial="string.printable"/>
                    </sanitizer>
                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                </param>
            </repeat>
            <repeat name="kmer_lengths" help="[optional]  Sequence kmer lengths to optionally use for entropy calculation. Warning: kmer entropy calculations may be time-consuming for large sequence sets." title="kmer_lengths: List[Int % Range(1, None)]">
                <param name="element" type="integer" min="1" value="" label="element: Int % Range(1, None)" help="[required]"/>
            </repeat>
            <param name="subsample_kmers" type="float" min="1e-06" max="1" value="1.0" label="subsample_kmers: Float % Range(0, 1, inclusive_start=False, inclusive_end=True)" help="[default: 1.0]  Optionally subsample sequences prior to kmer entropy measurement. A fraction of the input sequences will be randomly subsampled at the specified value."/>
            <param name="palette" type="select" label="palette: Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'cividis', 'terrain', 'rainbow', 'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic')">
                <option value="Set1">Set1</option>
                <option value="Set2">Set2</option>
                <option value="Set3">Set3</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel2">Pastel2</option>
                <option value="Paired">Paired</option>
                <option value="Accent">Accent</option>
                <option value="Dark2">Dark2</option>
                <option value="tab10">tab10</option>
                <option value="tab20">tab20</option>
                <option value="tab20b">tab20b</option>
                <option value="tab20c">tab20c</option>
                <option value="viridis" selected="true">viridis</option>
                <option value="plasma">plasma</option>
                <option value="inferno">inferno</option>
                <option value="magma">magma</option>
                <option value="cividis">cividis</option>
                <option value="terrain">terrain</option>
                <option value="rainbow">rainbow</option>
                <option value="PiYG">PiYG</option>
                <option value="PRGn">PRGn</option>
                <option value="BrBG">BrBG</option>
                <option value="PuOr">PuOr</option>
                <option value="RdGy">RdGy</option>
                <option value="RdBu">RdBu</option>
                <option value="RdYlBu">RdYlBu</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="Spectral">Spectral</option>
                <option value="coolwarm">coolwarm</option>
                <option value="bwr">bwr</option>
                <option value="seismic">seismic</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript evaluate-seqs
===============================
Compute summary statistics on sequence artifact(s).


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
Compute summary statistics on sequence artifact(s) and visualize. Summary statistics include the number of unique sequences, sequence entropy, kmer entropy, and sequence length distributions. This action is useful for both reference taxonomies and classification results.


|  

</help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>