comparison kobas_macros.xml @ 4:20f1b45dea63 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

3:83b998fa34ea

<macros>
    <token name="@WRAPPER_VERSION@">0.4</token>
    <token name="@KOBAS_VERSION@">2.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
        </requirements>
    </xml>
    <xml name="input_kobasdb">
        <param
            name="species"
            type="text"
            label="Species abbreviation"
            argument="--species"
            help="For example: ko for KEGG
                        Orthology, hsa for Homo sapiens, mmu for Mus musculus,
                        dme for Drosophila melanogaster, ath for Arabidopsis
                        thaliana, sce for Saccharomyces cerevisiae and eco for
                        Escherichia coli K-12 MG1655"/>
        <param format="sqlite" name="kobasdb" type="data" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
    </xml>
    <xml name="blastdb_selector">
        <param name="choice" type="select" label="BLAST Protein database">
            <option value="histdb">BLAST database from your history</option>
            <option value="fasta">BLAST database from FASTA File</option>
            <option value="local" selected="True">Locally installed BLAST database</option>
        </param>
        <when value="fasta">
            <param name="fastadb" format="fasta" type="data" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/>
            <param name="histdb" type="hidden" value=""/>
            <param name="fasta" type="hidden" value=""/>
        </when>
        <when value="histdb">
            <param name="localdb" type="hidden" value=""/>
            <param name="fastadb" type="hidden" value=""/>
            <param
                name="histdb"
                type="data"
                format="blastdbp"
                label="Protein BLAST database"
                help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
        </when>
        <when value="local">
            <param name="localdb" type="select" label="Protein BLAST database">
                <options from_data_table="blastdb_p"/>
            </param>
            <param name="histdb" type="hidden" value=""/>
            <param name="fastadb" type="hidden" value=""/>
        </when>
    </xml>
    <xml name="kobas_citations">
        <citations>
            <citation type="doi">10.1093/nar/gkr483</citation>

4:20f1b45dea63

<macros>
    <token name="@TOOL_VERSION@">2.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">kobas</requirement>
            <!-- kobas 2.1.1 is not compatible with Biopython >=1.73 due to https://github.com/biopython/biopython/issues/1952 -->
            <requirement type="package" version="1.72">biopython</requirement>
            <!-- Help conda resolving the enviroment, hopefully this can be removed for next update -->
            <requirement type="package" version="3.4">r-base</requirement>
        </requirements>
    </xml>
    <xml name="input_kobasdb">
        <param argument="--species" type="text" label="Species abbreviation"
            help="For example: ko for KEGG Orthology, hsa for Homo sapiens, mmu
                for Mus musculus, dme for Drosophila melanogaster, ath for
                Arabidopsis thaliana, sce for Saccharomyces cerevisiae and eco
                for Escherichia coli K-12 MG1655"/>
        <param name="kobasdb" type="data" format="sqlite" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
    </xml>
    <xml name="blastdb_selector">
        <param name="choice" type="select" label="BLAST Protein database">
            <option value="histdb">BLAST database from your history</option>
            <option value="fasta">BLAST database from FASTA File</option>
            <option value="local" selected="True">Locally installed BLAST database</option>
        </param>
        <when value="fasta">
            <param name="fastadb" type="data" format="fasta" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/>
        </when>
        <when value="histdb">
            <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database"
                help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
        </when>
        <when value="local">
            <param name="localdb" type="select" label="Protein BLAST database">
                <options from_data_table="blastdb_p"/>
            </param>
        </when>
    </xml>
    <xml name="kobas_citations">
        <citations>
            <citation type="doi">10.1093/nar/gkr483</citation>