<tool id="plant_tribes_gene_family_scaffold_updater" name="Update PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0">
    <description>with a new genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.7.1">blast</requirement>
        <requirement type="package" version="3.1b2">hmmer</requirement>
        <requirement type="package" version="7.313">mafft</requirement>
        <requirement type="package" version="5.22.0">perl</requirement>
        <requirement type="package" version="1.641">perl-dbi</requirement>
        <requirement type="package" version="3.5.3">perl-dbd-pg</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
perl '$__tool_directory__/gene_family_scaffold_updater.pl'
--database_connection_string '$__app__.config.plant_tribes_database_connection'
--proteins '$input_proteins'
--coding_sequences '$input_coding_sequences'
--scaffold '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold'
--species_name '$species_name'
--species_code '$species_code'
--species_family '$species_family'
--species_order '$species_order'
--species_group '$species_group'
--species_clade '$species_clade'
--rooting_order_species_code '$rooting_order_species_code'
--num_threads \${GALAXY_SLOTS:-4}
&>'$output']]></command>
    <inputs>
        <expand macro="param_scaffold"/>
        <param name="input_proteins" format="fasta" type="data" label="Proteins fasta file">
            <validator type="empty_field"/>
        </param>
        <param name="input_coding_sequences" format="fasta" type="data" label="Coding sequences fasta file">
            <validator type="empty_field"/>
        </param>
        <param name="species_name" type="text" value="" label="Species name">
            <validator type="empty_field"/>
        </param>
        <param name="species_code" type="text" value="" label="Species code">
            <validator type="empty_field"/>
        </param>
        <param name="species_family" type="text" value="" label="Species family">
            <validator type="empty_field"/>
        </param>
        <param name="species_order" type="text" value="" label="Species order">
            <validator type="empty_field"/>
        </param>
        <param name="species_group" type="text" value="" label="Species group">
            <validator type="empty_field"/>
        </param>
        <param name="species_clade" type="text" value="" label="Species clade">
            <validator type="empty_field"/>
        </param>
        <param name="rooting_order_species_code" type="text" label="Species code for rooting order" help="The new species above will be placed immediately after this species code in the rooting order configuration file">
            <validator type="empty_field"/>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="txt"/>
    </outputs>
    <tests>
        <test>
            <!--Testing this tool is a bit difficult at the current time.-->
        </test>
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
analyses of genome-scale gene families and transcriptomes. This tool adds a new genome to a scaffold installed into Galaxy
by the PlantTribes Scaffolds Downloader data manager tool.

-----

**Required options**

 * **Proteins fasta file** - amino acids (proteins) sequences fasta file for new genome.
 * **Coding sequences fasta file** - corresponding coding sequences (CDS) fasta file for new genome.
 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds, installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Eric Wafula},
            title = {None},
            year = {None},
            eprint = {None},
            url = {https://github.com/dePamphilis/PlantTribes}}
        </citation>
    </citations>
</tool>