comparison humann.xml @ 4:95bf7479d53c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0a3abeca0535457ddf39c394001d61cd2e45afdd

3:037c0b25c041

                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
                            <options from_data_table="metaphlan_database">
                                <validator message="No MetaPhlAn database is available" type="no_options" />
                            </options>
                        </param>
                    </when>
                    <when value="history">
                        <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>

            <param argument="--nucleotide-database" type="data_collection" collection_type="list" format="fasta" label="Nucleotide database from history" help="Each file must be named: ^[g__].[s__]"/>
        </xml>
        <xml name="nucleotide_search">
            <section name="nucleotide_search" title="Nucleotide search / Mapping reads to community pangenomes"  expanded="true">
                <conditional name="nucleotide_db">
                    <param name="selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
                        <option value="cached" selected="true">Locally cached</option>
                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="nucleotide_database" type="select" label="Nucleotide database">

            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            ]]></token>
        <xml name="translated_search">
            <section name="translated_search" title="Translated search / Aligning unmapped reads to a protein database" expanded="true">
                <conditional name="protein_db">
                    <param name="selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN2 databases">
                        <option value="cached" selected="true">Locally cached</option>
                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="protein_database" type="select" label="Protein database">

4:95bf7479d53c

                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
                            <options from_data_table="metaphlan_database">
                                <filter type="regexp" column="0" value=".*(vOct22_SGB|TOY|demo-db).*"/>
                                <validator message="No MetaPhlAn database is available" type="no_options"/>
                            </options>
                        </param>
                    </when>
                    <when value="history">
                        <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>

            <param argument="--nucleotide-database" type="data_collection" collection_type="list" format="fasta" label="Nucleotide database from history" help="Each file must be named: ^[g__].[s__]"/>
        </xml>
        <xml name="nucleotide_search">
            <section name="nucleotide_search" title="Nucleotide search / Mapping reads to community pangenomes"  expanded="true">
                <conditional name="nucleotide_db">
                    <param name="selector" type="select" label="Nucleotide database" help="For locally cached databases, you need first to execute the tool to download HUMAnN databases">
                        <option value="cached" selected="true">Locally cached</option>
                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="nucleotide_database" type="select" label="Nucleotide database">

            --nucleotide-query-coverage-threshold $wf.nucleotide_search.nucleotide_query_coverage_threshold
            ]]></token>
        <xml name="translated_search">
            <section name="translated_search" title="Translated search / Aligning unmapped reads to a protein database" expanded="true">
                <conditional name="protein_db">
                    <param name="selector" type="select" label="Protein database" help="For locally cached databases, you need first to execute the tool to download HUMAnN databases">
                        <option value="cached" selected="true">Locally cached</option>
                        <option value="history">From history</option>
                    </param>
                    <when value="cached">
                        <param name="protein_database" type="select" label="Protein database">