comparison qiime2_dbotu_q2.xml @ 0:9cb2b2d4dd8d draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ commit 2debd4e58ae65cf8a51a90a69768b6ae0716d270

0:9cb2b2d4dd8d

<tool name="qiime2 dbOTU" id="qiime2_dbotu_q2" version="2022.11.1+galaxy0" profile="22.05">
    <description>QIIME 2 plugin for distribution-based clustering</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">sebimer/samba-v4-qiime2:2022.11</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export NUMBA_CACHE_DIR=\$HOME &&
        ln -s '$input_table' input_table.qza &&
        ln -s '$input_seqs' input_seqs.qza &&
        qiime dbotu-q2 call-otus --i-table input_table.qza --i-sequences input_seqs.qza --p-gen-crit '$gen_crit' --p-abund-crit '$abund_crit' --p-pval-crit '$pval_crit' --o-dbotu-table output_table.qza --o-representative-sequences output_seqs.qza &&
        mv output_table.qza '$output_table' &&
        mv output_seqs.qza '$output_seqs'
    ]]></command>
    <inputs>
        <param name="input_table" type="data" format="qza" label="Table" help="The feature table containing counts for the dereplicated sequences (e.g. 100% OTUs or ASVs). Type: FeatureTable[Frequency]" />
        <param name="input_seqs" type="data" format="qza" label="Sequence" help="Input sequences. These should be either dereplicated (i.e. 100% OTUs) or exact sequence variants (i.e. output from deblur or DADA2 denoising). Type: FeatureData[Sequence]" />
        <param name="gen_crit" label="Genetic criterion" type="float" value="0.1" />
        <param name="abund_crit" label="Abundance criterion" type="float" value="10.0" min="0" />
        <param name="pval_crit" label="P-value criterion" type="float" value="0.0005" min="0" max="1" />
    </inputs>
    <outputs>
        <data name="output_table" format="qza" label="${tool.name} on ${on_string}: Feature table" />
        <data name="output_seqs" format="qza" label="${tool.name} on ${on_string}: Representative sequences" />
    </outputs>
    <tests>
        <test>
            <param name="input_table" value="counts.qza" ftype="qza"/>
            <param name="input_seqs" value="seq.qza" ftype="qza"/>
            <output name="output_table" ftype="qza">
                <assert_contents>
                    <has_size size="19254" />
                </assert_contents>
            </output>
            <output name="output_seqs" ftype="qza">
                <assert_contents>
                    <has_size size="16648" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
QIIME 2: dbOTU3
================================
q2-dbotu is a Qiime 2 plugin for performing OTU clustering using the distribution-based OTU (dbOTU) algorithm.

Outputs:
--------
- Feature table with sample counts for dbOTUs.
- Representative sequences for each dbOTU.

License (qiime2)
----------------
* `BSD 3-Clause license <https://raw.githubusercontent.com/qiime2/qiime2/refs/heads/dev/LICENSE>`_

License (q2-dbotu plugin)
-------------------------
* `MIT license <https://raw.githubusercontent.com/cduvallet/q2-dbotu/refs/heads/master/LICENSE>`_
]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
        <citation type="doi">10.1371/journal.pone.0176335</citation>
    </citations>
</tool>