<?xml version='1.0' encoding='UTF-8'?>
<macros>
    <token name="@WRAPPER_VERSION@">0.8</token>
    <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_aligner">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_classifier">
        <requirements>
            <requirement type="package" version="0.8">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="requirements_kaks_analysis">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
        </requirements>
    </xml>
    <xml name="requirements_gene_family_phylogeny_builder">
        <requirements>
            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</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_codon_alignments">
        <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
            <option value="yes" selected="true">Yes</option>
            <option value="no">No</option>
        </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_options_type">
        <param name="options_type" type="select" label="Options Configuration">
            <option value="basic" selected="true">Basic</option>
            <option value="advanced">Advanced</option>
        </param>
    </xml>
    <xml name="param_orthogroup_fna">
        <param name="orthogroup_fna" type="select" 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="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="cond_alignment_method">
        <conditional name="alignment_method_cond">
            <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
                <option value="mafft" selected="true">MAFFT algorithm</option>
                <option value="pasta">PASTA algorithm</option>
            </param>
            <when value="mafft" />
            <when value="pasta">
                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
            </when>
        </conditional>
    </xml>
    <xml name="cond_remove_gappy_sequences">
        <conditional name="remove_gappy_sequences_cond">
            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <conditional name="trim_type_cond">
                    <param name="trim_type" type="select" label="Select process used for trimming">
                        <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
                    </param>
                    <when value="gap_trimming">
                        <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
                    </when>
                    <when value="automated_trimming" />
                </conditional>
                <conditional name="remove_sequences_with_gaps_cond">
                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
                        <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
                    </when>
                </conditional>
            </when>
        </conditional>
    </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>