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<tool id="plant_tribes_gene_family_integrator" name="GeneFamilyIntegrator" version="@WRAPPER_VERSION@.0">
    <description>integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_gene_family_integrator" />
    <command detect_errors="exit_code"><![CDATA[
#set input_format = $input_format_cond.input_format
#set scaffold = $input_format_cond.scaffold
#set method = $input_format_cond.method

python '$__tool_directory__/gene_family_integrator.py'
--scaffold '$scaffold.fields.path'
--method $method
#if str($input_format) == 'ptortho':
    --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
    --output '$output_ptortho'
    --output_dir '$output_ptortho.files_path'
#else:
    ## str($input_format) == 'ptorthocs'
    --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
    #if str($input_format_cond.orthogroup_fna) == 'yes':
        --orthogroup_fna true
        --output '$output_ptorthocs'
        --output_dir '$output_ptorthocs.files_path'
    #else:
        --output '$output_ptortho'
        --output_dir '$output_ptortho.files_path'
    #end if
#end if
    ]]></command>
    <inputs>
        <conditional name="input_format_cond">
            <param name="input_format" type="select" label="Classified orthogroup fasta files">
                <option value="ptortho">Proteins orthogroup fasta files</option>
                <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
            </param>
            <when value="ptortho">
                <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
                    <validator type="empty_extra_files_path" />
                </param>
                <expand macro="param_scaffold" />
                <expand macro="param_method" />
            </when>
            <when value="ptorthocs">
                <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
                    <validator type="empty_extra_files_path" />
                </param>
                <expand macro="param_scaffold" />
                <expand macro="param_method" />
                <expand macro="param_orthogroup_fna" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_ptortho" format="ptortho" label="${tool.name} (integrated gene family clusters) on ${on_string}">
            <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter>
        </data>
        <data name="output_ptorthocs" format="ptorthocs" label="${tool.name} (integrated gene family clusters) on ${on_string}">
            <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
        <test>
        </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 integrates PlantTribes scaffold orthogroup backbone
gene models with gene coding sequences classified into the scaffold by the GeneFamilyClassifier tool.

-----

**Required options**

 * **Classified orthogroup fasta files** - orthogroup fasta files produced by the GeneFamilyClassifier tool selected from your history.  Depending on how the GeneFamilyClassifier tool was executed, these could either be proteins or proteins and their corresponding coding sequences.

 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.

**Other options**

 * **Orthogroups coding sequences** - Select 'Yes' to create corresponding coding sequences orthogroup fasta files for the classified protein sequences.

    </help>
    <citations>
        <expand macro="citation1" />
        <citation type="bibtex">
            @article{Wall2008,
            journal = {Nucleic Acids Research},
            author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
            title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
            year = {2008},
            volume = {36},
            number = {suppl 1},
            pages = {D970-D976},}
        </citation>
        <citation type="bibtex">
            @article{Sasidharan2012,
            journal = {Nucleic Acids Research},
            author = {3. 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 = {4. 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 = {5. 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>
    </citations>
</tool>