comparison funannotate_annotate.xml @ 12:732927f5b015 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

11:9c15ca7e764e

    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
## Needed by some subprocess invoked internally
## https://github.com/nextgenusfs/funannotate/issues/905
export FUNANNOTATE_DB='$database.fields.path'

&&

funannotate annotate

#if $input.input_type == 'gbk'
    --genbank '${input.genbank}'

        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />
                <filter type="sort_by" column="0" />
                <filter type="static_value" column="2" value="1.0" />
            </options>
        </param>

        <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />

12:732927f5b015

    </requirements>
    <version_command>funannotate check --show-versions</version_command>
    <command><![CDATA[
## Needed by some subprocess invoked internally
## https://github.com/nextgenusfs/funannotate/issues/905
export FUNANNOTATE_DB='$database.fields.path' &&

## show detailed info about the reference DB on stdout
funannotate database &&

funannotate annotate

#if $input.input_type == 'gbk'
    --genbank '${input.genbank}'

        <param name="database" label="Funannotate database" type="select">
            <options from_data_table="funannotate">
                <column name="value" index="0" />
                <column name="name" index="1" />
                <column name="path" index="3" />
                <filter type="sort_by" column="0" reverse_sort_order="true"/>
                <filter type="static_value" column="2" value="1.0" />
            </options>
        </param>

        <param argument="--sbt" type="data" format="txt" optional="true" label="NCBI submission template file" help="Create it on https://submit.ncbi.nlm.nih.gov/genbank/template/submission/ (or leave empty to use a default one, not suitable for submission at NCBI)" />