<tool id="plant_tribes_kaks_analysis" name="Perform orthologous or paralogous ks analyses" version="0.8.0">
    <description>of coding sequences and amino acid sequences</description>
    <requirements>
        <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->
        <regex match="Error:" />
        <regex match="Exception:" />
    </stdio>
    <command>
        <![CDATA[
            #set output_dir = 'kaksAnalysis_dir'
            #set comparison = $comparison_cond.comparison
            #if str($options_type.options_type_selector) == 'advanced':
                #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
                #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
                #set fit_components_cond = $options_type.fit_components_cond
                #set fit_components = $fit_components_cond.fit_components
                #set recalibrate_cond = $options_type.recalibrate_cond
                #set recalibrate = $recalibrate_cond.recalibrate
                #set set_min_coverage_cond = $options_type.set_min_coverage_cond
                #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
            #else:
                #set codeml_ctl_file_select = 'no'
                #set fit_components = 'no'
            #end if
            KaKsAnalysis
            --config_dir '$scaffold.fields.path'
            --num_threads \${GALAXY_SLOTS:-4}
            --coding_sequences_species_1 '$coding_sequences_species_1'
            --proteins_species_1 '$proteins_species_1'
            --comparison $comparison
            #if str($comparison) == 'orthologs':
                --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
                --proteins_species_2 '$comparison_cond.proteins_species_2'
            #end if
            #if str($options_type.options_type_selector) == 'advanced':
                #if str($set_min_coverage) == 'yes':
                    --min_coverage $set_min_coverage_cond.min_coverage
                #end if
                #if str($recalibrate) == 'yes':
                    --recalibration_rate $recalibrate_cond.recalibration_rate
                #end if
                #if str($codeml_ctl_file_select) == 'yes':
                    --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
                    # No else block needed here because the default codeml_ctl config
                    # will be used if the --codeml_ctl_file flag is missing.
                #end if
                #if str($fit_components) == 'yes':
                    --fit_components
                    --num_of_components $fit_components_cond.num_of_components
                    --min_ks $fit_components_cond.min_ks
                    --max_ks $fit_components_cond.max_ks
                #end if
            #end if
            >/dev/null
            && mv $output_dir/species1.fna '$output_species1_fna'
            && mv $output_dir/species1.faa '$output_species1_faa'
            #if str($comparison) == 'paralogs':
                && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
            #else:
                && mv $output_dir/species2.faa '$output_species2_faa'
                && mv $output_dir/species2.fna '$output_species2_fna'
                && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
                && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
            #end if
            && mv $output_dir/*.rbhb '$output_rbhb'
            && mv $output_dir/*.kaks '$output_kaks'
            #if str($fit_components) == 'yes':
                && mv $output_dir/*.components '$output_components'
            #end if
        ]]>
    </command>
    <inputs>
        <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
        <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
        <conditional name="comparison_cond">
            <param name="comparison" type="select" label="Select method for pairwise sequence comparison to determine homolgous pairs" help="Cross species comparison requires selection of inputs for second species">
                <option value="paralogs" selected="true">Self species comparison</option>
                <option value="orthologs">Cross species comparison</option>
            </param>
            <when value="paralogs" />
            <when value="orthologs">
                <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" />
                <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
            </when>
        </conditional>
        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
            <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>
        <conditional name="options_type">
            <param name="options_type_selector" type="select" label="Options Configuration">
                <option value="basic" selected="true">Basic</option>
                <option value="advanced">Advanced</option>
            </param>
            <when value="basic" />
            <when value="advanced">
                <conditional name="set_min_coverage_cond">
                    <param name="set_min_coverage" type="select" label="Specify minimum sequence pairwise coverage length between homologous pairs?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" />
                    </when>
                </conditional>
                <conditional name="recalibrate_cond">
                    <param name="recalibrate" type="select" label="Specify evolutionary rate for recalibrating synonymous subsitutions (ks) of species?">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
                    </when>
                </conditional>
                <conditional name="codeml_ctl_file_cond">
                    <param name="codeml_ctl_file_select" type="select" label="Select PAML codeml control file?" help="Used for ML analysis of protein-coding DNA sequences using codon substitution models, select No to use the default control file">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="codeml_ctl_file" format="txt" type="data" label="PAML codeml control file" />
                    </when>
                </conditional>
                <conditional name="fit_components_cond">
                    <param name="fit_components" type="select" label="Fit a mixture model of multivariate normal components to synonymous (ks) distribution?" help="Used to identify significant duplication events in a genome">
                        <option value="no" selected="true">No</option>
                        <option value="yes">Yes</option>
                    </param>
                    <when value="no" />
                    <when value="yes">
                        <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" />
                        <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome" />
                        <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" help="Excludes likey ancient paralogous pairs" />
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_species1_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}" />
        <data name="output_species1_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}" />
        <data name="output_species2_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}">
            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
        </data>
        <data name="output_species2_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}">
            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
        </data>
        <data name="output_species1_paralog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
            <filter>comparison_cond['comparison'] == 'paralogs'</filter>
        </data>
        <data name="output_species1_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
        </data>
        <data name="output_species2_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
            <filter>comparison_cond['comparison'] == 'orthologs'</filter>
        </data>
        <data name="output_rbhb" format="tabular" label="KaKs analysis (paralogous pairs) on ${on_string}" />
        <data name="output_kaks" format="tabular" label="KaKs analysis on ${on_string}" />
        <data name="output_components" format="tabular" label="KaKs analysis (significant components in the ks distribution) on ${on_string}">
            <filter>options_type[options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes</filter>
        </data>
    </outputs>
    <tests>
        <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. This tool performs orthologous
or paralogous ks analyses of coding sequences and amino acid sequences.

-----

**Options**

 * **Required options**

  - **Coding sequences (CDS) fasta file for the species** - Coding sequences (CDS) fasta file for the first species.
  - **Aamino acids (proteins) sequences fasta file for the species** - Aamino acids (proteins) sequences fasta file for the first species
  - **Select method for pairwise sequence comparison to determine homolgous pairs** - Pairwise sequence comparison to determine homolgous pairs (cross species comparison requires selection of inputs for second species).
  - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.

 * **Other (optional) options**

  - **Minimum sequence pairwise coverage length between homologous pairs** - Minimum sequence pairwise coverage length between homologous pairs (e.g., 0.5 results in 50% coverage.  Legal values lie between 0.3 and 1.0.
  - **Evolutionary rate for recalibrating synonymous subsitutions (ks) of species** - (applies to paralogous ks analysis) Recalibrate synonymous subsitutions (ks) of species using a predetermined evoutionary rate that can be determined from a species tree inferred from a collection single copy genes from taxa of interest (Cui et al., 2006).
  - **Select PAML codeml control file?** - Select PAML's codeml control file from your history.  This file is used to to perfom ML analysis of protein-coding DNA sequences using codon substitution models.  Selecting No uses the default file which does not include input (seqfile, treefile) and output (outfile) parameters of codeml.
  - **Fit a mixture model of multivariate normal components to synonymous (ks) distribution?** - Fit a mixture model of multivariate normal components to synonymous (ks) distribution to identify significant duplication event(s) in a genome.
  - **Number components to fit to synonymous subsitutions (ks) distribution** - Number components to fit to synonymous subsitutions (ks) distribution.
  - **Lower limit of synonymous subsitutions (ks)** - Lower limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to reduce background noise from young paralogous pairs due to normal gene births and deaths in a genome.
  - **Upper limit of synonymous subsitutions (ks)** - Upper limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to exclude likey ancient paralogous pairs.

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Eric Wafula},
            title = {None},
            year = {None},
            url = {https://github.com/dePamphilis/PlantTribes}
            }
        </citation>
        <citation type="doi">10.1093/bioinformatics/btw412</citation>
        <citation type="doi">10.1186/1471-2105-10-421</citation>
        <citation type="doi">10.1093/molbev/msm088</citation>
        <citation type="doi">10.18637/jss.v004.i02</citation>
    </citations>
</tool>