<tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.0">
    <description>builds gene family phylogenetic trees</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_gene_family_phylogeny_builder" />
    <expand macro="stdio" />
    <command>
        <![CDATA[
            #set input_format = $input_format_cond.input_format
            #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
            #set tree_inference = $tree_inference_cond.tree_inference
            #if str($tree_inference) == 'raxml':
                #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
                #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
                #if str($rooting_order_file) == 'yes':
                    #set rooting_order = $rooting_order_file_cond.rooting_order
                #end if
                #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
            #end if

            python $__tool_directory__/gene_family_phylogeny_builder.py
            --orthogroup_aln '$input_aln.extra_files_path'
            --scaffold '$scaffold.fields.path'
            --config_dir '$scaffold.fields.path'
            --method $method
            --tree_inference $tree_inference
            #if str($tree_inference) == 'raxml':
                #if str($rooting_order_file) == 'yes':
                    --rooting_order '$rooting_order'
                    ## No else block needed here because the default rooting_order
                    ## configuration will be used if the --rooting_order flag is missing.
                #end if
                --bootstrap_replicates $bootstrap_replicates
            #end if
            --min_orthogroup_size $min_orthogroup_size
            --max_orthogroup_size $max_orthogroup_size
            --num_threads \${GALAXY_SLOTS:-4}
            #if str($input_format) == 'ptalign':
                --alignment_type 'aln'
                --sequence_type 'protein'
            #else if str($input_format) == 'ptalignca':
                --alignment_type 'aln'
                --sequence_type $input_format_cond.sequence_type
            #else if str($input_format) == 'ptalignfiltered':
                --alignment_type 'filter'
                --sequence_type 'protein'
            #else if str($input_format) == 'ptalignfilteredca':
                --alignment_type 'filter'
                --sequence_type $input_format_cond.sequence_type
            #else if str($input_format) == 'ptaligntrimmed':
                --alignment_type 'trim'
                --sequence_type 'protein'
            #else if str($input_format) == 'ptaligntrimmedca':
                --alignment_type 'trim'
                --sequence_type $input_format_cond.sequence_type
            #end if
            --output '$output_pttree'
            --output_dir '$output_pttree.files_path'
        ]]>
    </command>
    <inputs>
        <conditional name="input_format_cond">
            <param name="input_format" type="select" label="Select type of data">
                <option value="ptalign">Aligned gene family sequences</option>
                <option value="ptalignca">Aligned gene family sequences with codon alignments</option>
                <option value="ptalignfiltered">Filtered aligned gene family sequences</option>
                <option value="ptalignfilteredca">Filtered aligned gene family sequences with codon alignments</option>
                <option value="ptaligntrimmed">Trimmed aligned gene family sequences</option>
                <option value="ptaligntrimmedca">Trimmed aligned gene family sequences with codon alignments</option>
            </param>
            <when value="ptalign">
                <param name="input_ptalign" format="ptalign" type="data" label="Aligned gene family sequences">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
            </when>
            <when value="ptalignca">
                <param name="input_ptalignca" format="ptalignca" type="data" label="Aligned gene family sequences with codon alignments">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
                <expand macro="param_sequence_type" />
            </when>
            <when value="ptalignfiltered">
                <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered aligned gene family sequences">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
            </when>
            <when value="ptalignfilteredca">
                <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered aligned gene family sequences with codon alignments">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
                <expand macro="param_sequence_type" />
            </when>
            <when value="ptaligntrimmed">
                <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed aligned gene family sequences">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
            </when>
            <when value="ptaligntrimmedca">
                <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed aligned gene family sequences with codon alignments">
                    <!-- <validator type="empty_files_path" /> -->
                </param>
                <expand macro="param_sequence_type" />
            </when>
        </conditional>
        <expand macro="param_scaffold" />
        <expand macro="param_method" />
        <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" />
    </inputs>
    <outputs>
        <data name="output_pttree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
    </outputs>
    <tests>
        <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
        <test>
        </test>
        -->
    </tests>
    <help>
This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of
complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
**GeneFamilyAligner** tool.

-----

**Required options**

**Other options**

    </help>
    <citations>
        <expand macro="citation1" />
        <expand macro="citations2to4" />
    </citations>
</tool>