Merge pull request #1596 from RZ9082/qiime2_dbotu

Add Qiime2 dbotu plugin

Author: RZ9082

tools/qiime2_dbotu_q2/.shed.yml

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+name: qiime2_dbotu_q2
+owner: bgruening
+description: q2-dbotu is a Qiime 2 plugin for performing OTU clustering
+homepage_url: https://github.com/cduvallet/q2-dbotu/tree/master
+long_description: |
+  q2-dbotu is a Qiime 2 plugin for performing OTU clustering using the distribution-based OTU (dbOTU) algorithm.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/
+type: unrestricted
+categories:
+- Metagenomics

tools/qiime2_dbotu_q2/qiime2_dbotu_q2.xml

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+<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>