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<?xml version='1.0' encoding='UTF-8'?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</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_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="cond_multiple_sequence_alignments">
        <conditional name="multiple_sequence_alignments_cond">
            <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <conditional name="multiple_sequence_alignments_option_cond">
                    <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
                        <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
                        <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
                        <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
                    </param>
                    <when value="create_alignments" />
                    <when value="add_alignments" />
                    <when value="pasta_alignments">
                        <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="cond_phylogenomic_trees">
        <conditional name="phylogenetic_trees_cond">
            <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <conditional name="tree_inference_cond">
                    <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
                        <option value="raxml" selected="true">RAxML</option>
                        <option value="fasttree">FastTree</option>
                    </param>
                    <when value="raxml">
                        <conditional name="rooting_order_file_cond">
                            <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
                                <option value="no" selected="true">No</option>
                                <option value="yes">Yes</option>
                            </param>
                            <when value="no" />
                            <when value="yes">
                                <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
                            </when>
                        </conditional>
                        <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
                    </when>
                    <when value="fasttree" />
                </conditional>
                <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
                <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
            </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 gap trimming">
                        <option value="gap_trimming" selected="true">Nucleotide based </option>
                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
                    </param>
                    <when value="automated_trimming" />
                    <when value="gap_trimming">
                        <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
                    </when>
                </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="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
                        <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="cond_multiple_codon_alignments">
        <conditional name="multiple_codon_alignments_cond">
            <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
                    <option value="protein" selected="true">Amino acid based</option>
                    <option value="dna">Nucleotide based</option>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{None,
                journal = {None},
                author = {1. Wafula EK},
                title = {Manuscript in preparation},
                year = {None},
                url = {https://github.com/dePamphilis/PlantTribes},}
            </citation>
            <citation type="bibtex">
                @article{Mirarab2014,
                journal = {Research in Computational Molecular Biology (RECOMB)},
                author = {2. Mirarab S, Nguyen N, Warnow T},
                title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
                year = {2014},
                pages = {177–191},
                url = {https://github.com/smirarab/pasta},}
            </citation>
            <citation type="bibtex">
                @article{Salvador2009,
                journal = {Bioinformatics},
                author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
                title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
                year = {2009},
                url = {http://trimal.cgenomics.org},}
            </citation>
            <citation type="bibtex">
                @article{Stamatakis2014,
                journal = {Bioinformatics},
                author = {4. Stamatakis A},
                title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
                year = {2014},
                url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
            </citation>
            <citation type="doi">10.1371/journal.pone.0009490</citation>
            <citation type="doi">10.1093/bioinformatics/btw412</citation>
        </citations>
    </xml>
</macros>