comparison genomad_end_to_end.xml @ 1:edb671f0661e draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/genomad/ commit dddf8b42771f66318f3325607bbd7aa33a3716b5

0:955e33326e20

<tool id="genomad_end_to_end" name="geNomad" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
    <description>identify virus and plasmid genomes from nucleotide sequences</description>
    <macros>
        <token name="@TOOL_VERSION@">1.8.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@MIN_DB_VERSION@">1.2</token>  <!-- https://portal.nersc.gov/genomad/__data__/releases.txt -->
        <xml name="summary_output_macro" tokens="type">
            <data name="summary_@TYPE@_fna" format="fasta" from_work_dir="output/sequence_summary/sequence_@TYPE@.fna" label="${tool.name} on ${on_string}: @TYPE@ fasta"/>
            <data name="summary_@TYPE@_genes" format="tabular" from_work_dir="output/sequence_summary/sequence_@TYPE@_genes.tsv" label="${tool.name} on ${on_string}: @TYPE@ genes">
                <actions>

            sequence.fa
            output/
            '$DATABASE.fields.path'
    ]]></command>
    <inputs>
        <param argument="INPUT" type="data" format="fasta" label="Input sequences" help="geNomad will work for isolate genomes, metagenomes, and metatranscriptomes"/>
        <param name="DATABASE" type="select" label="Reference data" help="">
            <options from_data_table="genomad"/>
            <!-- TODO needs to be activated with https://github.com/galaxyproject/galaxy/pull/18411
                <validator type="in_range" min="@MIN_DB_VERSION@"/> -->

        <expand macro="summary_output_macro" type="plasmid"/>
        <expand macro="summary_output_macro" type="virus"/>
    </outputs>
    <tests>
        <test>
            <param name="INPUT" value="GCF_009025895.1_ASM902589v1_genomic.fna" ftype="fasta"/>
            <param name="DATABASE" value="1.2"/>
            <section name="annotation">
                <param name="splits" value="8"/><!-- needed for low mem CI-->
            </section>

geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences.
For details on the function refer to the citation or https://portal.nersc.gov/genomad/index.html.

This Galaxy tool executed the ent-to-end geNomad workflow.

Usage
.....

* annotation_description: A text describing the function assigned to the marker.


plasmid/virus genes/proteins: gives the nucleotide and aminoaced sequences of the annotated genes

    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-023-01953-y</citation>
    </citations>
</tool>

1:edb671f0661e

<tool id="genomad_end_to_end" name="geNomad" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
    <description>identify virus and plasmid genomes from nucleotide sequences</description>
    <macros>
        <token name="@TOOL_VERSION@">1.8.0</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <token name="@MIN_DB_VERSION@">1.2</token>  <!-- https://portal.nersc.gov/genomad/__data__/releases.txt -->
        <xml name="summary_output_macro" tokens="type">
            <data name="summary_@TYPE@_fna" format="fasta" from_work_dir="output/sequence_summary/sequence_@TYPE@.fna" label="${tool.name} on ${on_string}: @TYPE@ fasta"/>
            <data name="summary_@TYPE@_genes" format="tabular" from_work_dir="output/sequence_summary/sequence_@TYPE@_genes.tsv" label="${tool.name} on ${on_string}: @TYPE@ genes">
                <actions>

            sequence.fa
            output/
            '$DATABASE.fields.path'
    ]]></command>
    <inputs>
        <param name="license" type="boolean" checked="false" label="Agree with geNomad license?" help="geNomad is free to use for internal use, research &amp; development, non-commercial use, purposes only.">
            <validator type="expression" message="You need to agree to the geNomad license in order to use this tool. License is linked in the help below.">value</validator>
        </param>
        <param argument="INPUT" type="data" format="fasta" label="Input sequences" help="geNomad will work for isolate genomes, metagenomes, and metatranscriptomes"/>
        <param name="DATABASE" type="select" label="Reference data" help="">
            <options from_data_table="genomad"/>
            <!-- TODO needs to be activated with https://github.com/galaxyproject/galaxy/pull/18411
                <validator type="in_range" min="@MIN_DB_VERSION@"/> -->

        <expand macro="summary_output_macro" type="plasmid"/>
        <expand macro="summary_output_macro" type="virus"/>
    </outputs>
    <tests>
        <test>
            <param name="license" value="true"/>
            <param name="INPUT" value="GCF_009025895.1_ASM902589v1_genomic.fna" ftype="fasta"/>
            <param name="DATABASE" value="1.2"/>
            <section name="annotation">
                <param name="splits" value="8"/><!-- needed for low mem CI-->
            </section>

geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences.
For details on the function refer to the citation or https://portal.nersc.gov/genomad/index.html.

This Galaxy tool executed the ent-to-end geNomad workflow.

geNomad is free to use for internal use, research & development, non-commercial use, purposes **only**. Check out the full `License`_.

Usage
.....

* annotation_description: A text describing the function assigned to the marker.


plasmid/virus genes/proteins: gives the nucleotide and aminoaced sequences of the annotated genes

.. _License: https://raw.githubusercontent.com/apcamargo/genomad/refs/heads/main/LICENSE

    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-023-01953-y</citation>
    </citations>
</tool>