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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/marine_omics commit 9dff0476530d65342db00896f3108edb899e3fd2

<tool id="sanntis_marine" name="Sanntis biosynthetic gene clusters" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>in genomic and metagenomic data</description>
    <macros>
        <token name="@TOOL_VERSION@">0.9.3.5</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_3387</edam_topic>
    </edam_topics>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">sanntis</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    #if $selection.which_sanntis == 'sanntis': 
        sanntis --ip-file '$selection.input_interpro' --outfile 'output_sanntis.gff' '$selection.input_genbank'
    #else:
        sanntis_build_gb  -n '$selection.input_nuc' -a '$selection.input_prot' -o 'output_sanntis_gb.gb'
    #end if 
    ]]></command>
    <inputs>
        <conditional name="selection">
            <param name="which_sanntis" type="select" label="Do you want to build a genbank or to make a SMBGC Annotation?" help="If you decide to build a genbank you can then use this genbank to then conduct the annotation.">
                <option value="sanntis">Run sanntis</option>
                <option value="genbank">Build genbank</option>
            </param>
            <when value="sanntis">
                <param name="input_interpro" type="data" format="tabular" label="Input the tabular file from InterProScan" help="Before using this tool you need to retrieve the right data by using the InterProScan tool"/>
                <param name="input_genbank" type="data" format="genbank" label="Input a Genbank file" help="It needs to have the right structure and fit the protein fasta file used in InterProScan"/>
            </when>
            <when value="genbank">
                <param name="input_nuc" type="data" format="fasta" label="Input a nucleotide fasta file"/>
                <param name="input_prot" type="data" format="fasta" label="Input a protein fasta file" help="Before using this tool you can get the right protein data by using the Prodigal tool"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_sanntis" from_work_dir="output_sanntis.gff" format="gff3" label="Sanntis output data">
            <filter>selection['which_sanntis'] == 'sanntis'</filter>
        </data>
        <data name="output_sanntis_gb" from_work_dir="output_sanntis_gb.gb" format="genbank" label="Sanntis output data genbank">
            <filter>selection['which_sanntis'] == 'genbank'</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="which_sanntis" value="sanntis"/>
            <param name="input_interpro" value="BGC0001472.fna.prodigal.faa.ip.tsv"/>
            <param name="input_genbank" value="BGC0001472.fna.prodigal.faa.gb"/>
            <output name="output_sanntis" value="Sanntis_output_data.gff3"/>
        </test>
        <test expect_num_outputs="1">
            <param name="which_sanntis" value="genbank"/>
            <param name="input_nuc" value="BGC0001472.fna"/>
            <param name="input_prot" value="Regex_Find_And_Replace_on_data_21.fasta"/>
            <output name="output_sanntis_gb" value="Sanntis_output_data.genbank"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

SMBGC Annotation using Neural Networks Trained on Interpro Signatures
Tool for identifying biosynthetic gene clusters (BGCs) in genomic & metagenomic data

**Or**

This tool can also create a Genbank adapted to be used in sanntis

.....


**Input**
- A tsv file coming from InterProScan tool from which you can retrieve the right data.
- The right Genbank file with the right structure that fits the protein fasta file used to run InterProScan tool

**Output**
- A Gff3 file

    ]]></help>
    <citations>
        <citation type="doi">10.1101/2023.05.23.540769</citation>
    </citations>
</tool>