view qiime2__fragment_insertion__classify_otus_experimental.xml @ 0:4139c3491d30 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 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 fragment-insertion classify-otus-experimental" id="qiime2__fragment_insertion__classify_otus_experimental" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version fragment_insertion</version_command>
    <command detect_errors="aggressive">q2galaxy run fragment_insertion classify_otus_experimental '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="representative_sequences" type="data" format="qza" label="representative_sequences: FeatureData[Sequence]" help="[required]  The sequences used for a 'sepp' run to produce the 'tree'.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required]  The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
        </param>
        <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required]  Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Taxonomy]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="classification" format="qza" label="${tool.name} on ${on_string}: classification.qza" from_work_dir="classification.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: fragment-insertion classify-otus-experimental
======================================================
Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.


Outputs:
--------
:classification.qza: Taxonomic lineages for inserted fragments.

|  

Description:
------------
Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID for every inserted fragment. Then, look up the reference lineage string in the reference taxonomy.


|  

</help>
    <citations>
        <citation type="doi">10.1128/mSystems.00021-18</citation>
        <citation type="doi">10.1371/journal.pone.0031009</citation>
        <citation type="doi">10.1371/journal.pcbi.1002195</citation>
        <citation type="bibtex">@article{cite4,
 author = {Matsen, Frederick A and Kodner, Robin B and Armbrust, E Virginia},
 journal = {BMC bioinformatics},
 number = {1},
 pages = {538},
 publisher = {BioMed Central},
 title = {pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree},
 volume = {11},
 year = {2010}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>