<?xml version='1.0' encoding='UTF-8'?>
<macros>
    <xml name="requirements_assembly_post_processor">
        <requirements>
            <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_classifier">
        <requirements>
            <requirement type="package" version="0.4">plant_tribes_gene_family_classifier</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_integrator">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range="1:"/>
            <exit_code range=":-1"/>
            <regex match="Error:"/>
            <regex match="Exception:"/>
        </stdio>
    </xml>
    <xml name="param_scaffold">
        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
            <options from_data_table="plant_tribes_scaffolds" />
            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
        </param>
    </xml>
    <xml name="param_method">
        <param name="method" type="select" label="Protein clustering method">
            <option value="gfam" selected="true">GFam</option>
            <option value="orthofinder">OrthoFinder</option>
            <option value="orthomcl">OrthoMCL</option>
        </param>
    </xml>
    <xml name="param_orthogroup_fna">
        <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
        </param>
    </xml>
    <xml name="citation1">
        <citation type="bibtex">
            @misc{None,
            journal = {None},
            author = {1. Wafula EK},
            title = {Manuscript in preparation},
            year = {None},
            url = {https://github.com/dePamphilis/PlantTribes},}
        </citation>
    </xml>
    <xml name="citations2to4">
        <citation type="bibtex">
            @article{Sasidharan2012,
            journal = {Nucleic Acids Research},
            author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
            title = {GFam: a platform for automatic annotation of gene families},
            year = {2012},
            pages = {gks631},}
        </citation>
        <citation type="bibtex">
            @article{Li2003,
            journal = {Genome Research}
            author = {3. Li L, Stoeckert CJ, Roos DS},
            title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
            year = {2003},
            volume = {13},
            number = {9},
            pages = {2178-2189},}
        </citation>
        <citation type="bibtex">
            @article{Emms2015,
            journal = {Genome Biology}
            author = {4. Emms DM, Kelly S},
            title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
            year = {2015},
            volume = {16},
            number = {1},
            pages = {157},}
        </citation>
    </xml>
</macros>