comparison kaks_analysis.xml @ 37:b7a3dce9c4f7 draft

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36:ff040a476523

    <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_kaks_analysis" />
    <command detect_errors="exit_code">
        <![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
                #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond
                #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
                #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond
                #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
            #else:
                #set codeml_ctl_file_select = 'no'
                #set fit_components = 'no'
                #set set_lower_ks_limit = 'no'
                #set set_upper_ks_limit = 'no'
            #end if
            KaKsAnalysis
            --num_threads \${GALAXY_SLOTS:-4}
            --coding_sequences_species_1 '$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 $fit_components_cond.num_of_components
                #end if
                #if str($set_lower_ks_limit) == 'yes':
                    --min_ks $set_lower_ks_limit_cond.min_ks
                #end if
                #if str($set_upper_ks_limit) == 'yes':
                    --max_ks $set_upper_ks_limit_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 for the first species" />
        <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" />
        <conditional name="comparison_cond">
            <param name="comparison" type="select" label="Type of sequence comparison">

37:b7a3dce9c4f7

    <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements_kaks_analysis" />
    <command detect_errors="exit_code"><![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
    #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond
    #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
    #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond
    #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
#else:
    #set codeml_ctl_file_select = 'no'
    #set fit_components = 'no'
    #set set_lower_ks_limit = 'no'
    #set set_upper_ks_limit = 'no'
#end if
KaKsAnalysis
--num_threads \${GALAXY_SLOTS:-4}
--coding_sequences_species_1 '$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 $fit_components_cond.num_of_components
    #end if
    #if str($set_lower_ks_limit) == 'yes':
        --min_ks $set_lower_ks_limit_cond.min_ks
    #end if
    #if str($set_upper_ks_limit) == 'yes':
        --max_ks $set_upper_ks_limit_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 for the first species" />
        <param name="proteins_species_1" format="fasta" type="data" label="Protein sequences for the first species" />
        <conditional name="comparison_cond">
            <param name="comparison" type="select" label="Type of sequence comparison">