Mercurial > repos > bgruening > qiime2_dbotu_q2
changeset 0:9cb2b2d4dd8d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/qiime2_dbotu_q2/ commit 2debd4e58ae65cf8a51a90a69768b6ae0716d270
| author | bgruening |
|---|---|
| date | Mon, 24 Mar 2025 13:40:07 +0000 |
| parents | |
| children | |
| files | qiime2_dbotu_q2.xml test-data/counts.qza test-data/seq.qza |
| diffstat | 3 files changed, 66 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2_dbotu_q2.xml Mon Mar 24 13:40:07 2025 +0000 @@ -0,0 +1,66 @@ +<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>