comparison plink.xml @ 9:272aca44b3dd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"

8:16d22eee0fe3

<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
    <macros>
        <token name='@TOOL_VERSION@'>1.9.b618</token>
        <token name='@VERSION_SUFFIX@'>3</token>
        <xml name='template_sanitizer'>
            <sanitizer>
                <valid initial='default'>
                    <add value='#' />
                    <add value='@' />

                <valid initial='string.ascii_letters + string.digits'>
                    <add value=' '/>
                </valid>
            </sanitizer>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">plink</xref>
    </xrefs>
    <requirements>
        <requirement type='package' version='1.90b6.18'>plink</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[

    ## Create Plink folder for any inputs
    mkdir ./plink_output

    ## If bmerge is set, create folder for merged files
    #if $functions.func == 'data_manage':
        #if $functions.bmerge.set == 'Yes':
            && mkdir bmerge_files
            && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed
            && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim
            && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam
        #end if
    #end if


    #if $inputs.inputs.filetype == 'bfile':
        && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
        && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
        && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
        && plink --bfile plink_input/plink_input
    #elif $inputs.inputs.filetype == 'vcf':
        #if $inputs.inputs.input.is_of_type('bcf'):
            && plink --bcf '$inputs.inputs.input' 
        #else:

            && mkdir assoc_out
            && mv ./plink_output/*asso* assoc_out
            && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
        #end if
    #end if
    ]]></command>
    <inputs>
        <section name='inputs' title='Data inputs' expanded='true'>
            <conditional name='inputs'>
                <param name='filetype' type='select' label='Main input data type'>
                    <option value='bfile'>plink file</option>
                    <option value='vcf'>VCF input file</option>
                </param>
                <when value='bfile'>
                    <param format='pbed' name='bed' type='data' label='plink bed file'/>
                    <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
                    <param format='txt' name='fam' type='data' label='plink fam file'/>
                </when>
                <when value='vcf'>
                    <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
                </when>
            </conditional>

                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param format='binary' name='bed' type='data' label='plink bed file'/>
                        <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
                        <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/>
                    </when>
                </conditional>
                <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/>
                <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/>
                <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'>

                        <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/>
                        <param name='step' type='integer' label='Step size (variant ct)' value='5'/>
                        <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' />
                    </when>
                </conditional>

            </when>
            <when value='stratification'>
                <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
                <conditional name='cluster'>
                    <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>

            </when> -->
        </conditional>
    </inputs>
    <outputs>
        <!--Main-->
        <collection name='plink_out' type='list' label='Plink main outputs'>
            <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/>
            <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/>
            <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/>
            <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/>
        </collection>

        <!--Data Manage-->
        <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'>
            <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
        </data>
        <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'>
            <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
        </data>

        <!--Stats-->
        <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'>
            <filter>functions['func'] == 'stats' and functions['freq']</filter>
        </data>
        <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'>
            <filter>functions['func'] == 'stats' and functions['hardy']</filter>
        </data>
        <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'>
            <filter>functions['func'] == 'stats' and functions['missing']</filter>
        </data>
        <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'>
            <filter>functions['func'] == 'stats' and functions['missing']</filter>
        </data>
        <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'>
            <filter>functions['func'] == 'stats' and functions['het']</filter>
        </data>
        <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'>
            <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
        </data>
        
        <!--Association-->
            <!--Assoc -->

        <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'>
            <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs='5'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='filtering'/>
                <conditional name='id_list'>

                    <param name='sex_select' value='--filter-cases'/>
                    <param name='no_sex_select' value='--allow-no-sex'/>
                    <param name='nonfounders' value='--nonfounders'/>
                </conditional>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='test1_out.bed' compare='sim_size'/>
                <element name='plink_bim' file='test1_out.bim'/>
                <element name='plink_fam' file='test1_out.fam'/>
            </output_collection>
        </test>

        <test expect_num_outputs='7'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='data_manage'/>
                <conditional name='bmerge'>
                    <param name='set' value='Yes'/>
                    <param name='bed' value='plink_2.bed'/>
                    <param name='bim' value='plink_2.bim'/>
                    <param name='fam' value='plink_2.fam'/>
                </conditional>
                <param name='recode' value='--recode'/>
                <param name='template' value='@asd#123'/>
                <param name='length' value='23'/>
                <conditional name='update_cols'>

                    <param name='col_num' value='1'/>
                    <param name='var_col' value='2'/>
                    <param name='skip' value='a'/>
                </conditional>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='test2_out.bed' compare='sim_size'/>
                <element name='plink_bim' file='test2_out.bim'/>
                <element name='plink_fam' file='test2_out.fam'/>
            </output_collection>
            <output name='plink_ped' file='out.ped'/>
            <output name='plink_map' file='out.map'/>
        </test>

        <test expect_num_outputs='5'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='vcf'/>
                    <param name='input' value='test.vcf'/>
                </conditional>
            </section>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='vcf_out.bed'/>
                <element name='plink_bim' file='vcf_out.bim'/>
                <element name='plink_fam' file='vcf_out.fam'/>
            </output_collection>
        </test>

        <test expect_num_outputs='11'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='x_plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='stats'/>
                <param name='freq' value='--freq'/>

                        <param name='female_max_obvs' value='10'/>
                        <param name='male_min_obvs' value='200'/>
                    </conditional>
                </conditional>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='stats.bed'/>
                <element name='plink_bim' file='stats.bim'/>
                <element name='plink_fam' file='stats.fam'/>
                <element name='plink_fam' file='stats.fam'/>
            </output_collection>
            <output name='frequency' file='out.freq'/>
            <output name='hardy_out' file='out.hardy'/>
            <output name='missing_1' file='out.imiss'/>
            <output name='missing_2' file='out.lmiss'/>
            <output name='het' file='out.het'/>
            <output name='sex_check' file='out.sexcheck'/>
        </test>

        <test expect_num_outputs='7'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='link'/>
                <conditional name='set_indep'>

                    <param name='window' value='51'/>
                    <param name='step' value='6'/>
                    <param name='r2' value='0.3'/>
                </conditional>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='test5_out.bed' compare='sim_size'/>
                <element name='plink_bim' file='test5_out.bim'/>
                <element name='plink_fam' file='test5_out.fam'/>
            </output_collection>
            <output name='prune_in' file='plink.prune.in'/>
        </test>
        
        <test expect_num_outputs='10'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='stratification'/>
                <param name='read_genome' value='plink.genome'/>

                        <param name='dimensions' value='10'/>
                        <param name='modifiers' value='eigendecomp,eigvals'/>
                    </conditional>
                </conditional>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='test6_out.bed' compare='sim_size'/>
                <element name='plink_bim' file='test6_out.bim'/>
                <element name='plink_fam' file='test6_out.fam'/>
            </output_collection>
            <output name='mds' value='plink.mds' compare='sim_size'/>
            <output name='cluster1' value='plink.cluster1' compare='sim_size'/>
            <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
            <output name='cluster3' value='plink.cluster3' compare='sim_size'/>
            <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
        </test>

        <test expect_num_outputs='8'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='association'/>
                <conditional name='assoc'>

                    <param name='beta' value='beta'/>
                    <param name='intercept' value='intercept'/>
                </conditional>
                <param name='lambda' value='1.0'/>
            </conditional>
            <output_collection name='plink_out' type='list'>
                <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/>
                <element name='plink_bim' file='out.assoc.bim'/>
                <element name='plink_fam' file='out.assoc.fam'/>
            </output_collection>
            <output_collection name='assoc_outfiles'  type='list' count='2'>
                <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
                <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
            </output_collection>
            <output_collection name='adjust_outfiles' type='list' count='1'>

                <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/>
                <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/>
            </output_collection>
        </test>

        <test expect_num_outputs='6'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>
                    <param name='fam' value='plink.fam'/>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='ibd'/>
                <conditional name='genome'>

                    <param name='min' value='0.1'/>
                    <param name='max' value='0.9'/>
                    <param name='modifiers' value='full,unbounded,nudge'/>
                </conditional>
            </conditional>
            <output name='genome' file='out.genome'/>
        </test>
    </tests>
    <help><![CDATA[
        PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

9:272aca44b3dd

<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
    <macros>
        <token name='@TOOL_VERSION@'>1.90b6.21</token>
        <token name='@VERSION_SUFFIX@'>0</token>
        <xml name='template_sanitizer'>
            <sanitizer>
                <valid initial='default'>
                    <add value='#' />
                    <add value='@' />

                <valid initial='string.ascii_letters + string.digits'>
                    <add value=' '/>
                </valid>
            </sanitizer>
        </xml>
        <xml name="log_out_assert">
            <output name="plink_log">
                <assert_contents>
                    <has_text text="End time:"/>
                </assert_contents>
            </output>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">plink</xref>
    </xrefs>
    <requirements>
        <requirement type='package' version='@TOOL_VERSION@'>plink</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[

    ## Create Plink folder for any inputs
    mkdir ./plink_output

    ## If bmerge is set, create folder for merged files
    #if $functions.func == 'data_manage':
        #if $functions.bmerge.set == 'Yes':
            && mkdir bmerge_files
            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed
            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim
            && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam
        #end if
    #end if


    #if $inputs.inputs.filetype == 'bfile':
        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed
        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim
        && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam
        && plink --bfile plink_input/plink_input
    #elif $inputs.inputs.filetype == 'vcf':
        #if $inputs.inputs.input.is_of_type('bcf'):
            && plink --bcf '$inputs.inputs.input' 
        #else:

            && mkdir assoc_out
            && mv ./plink_output/*asso* assoc_out
            && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
        #end if
    #end if
    && mkdir '$plink_out.extra_files_path'
    && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed
    && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim
    && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam
    ]]></command>
    <inputs>
        <section name='inputs' title='Data inputs' expanded='true'>
            <conditional name='inputs'>
                <param name='filetype' type='select' label='Main input data type'>
                    <option value='bfile'>plink file</option>
                    <option value='vcf'>VCF input file</option>
                </param>
                <when value='bfile'>
                    <param format='pbed' name='bed' type='data' label='plink bed file'/>
                </when>
                <when value='vcf'>
                    <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
                </when>
            </conditional>

                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param format='pbed' name='bed' type='data' label='plink bed file'/>
                    </when>
                </conditional>
                <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/>
                <param format='tsv,tabular' name='flip' type='data' label='Flip DNA strand for SNPs' help='Given a file containing a list of SNPs with A/C/G/T alleles, --flip swaps A↔T and C↔G.' optional='true'/>
                <param name='template' type='text' label='Update Variant Info: Template String' help='Replaces missing IDs. The parameter taken by these flags is a special template string, with a @ where the chromosome code should go, and a # where the base-pair position belongs.'>

                        <param name='window' type='integer' label='Window size in bp' value='50' help='Window size'/>
                        <param name='step' type='integer' label='Step size (variant ct)' value='5'/>
                        <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' />
                    </when>
                </conditional>
            </when>
            <when value='stratification'>
                <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
                <conditional name='cluster'>
                    <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>

            </when> -->
        </conditional>
    </inputs>
    <outputs>
        <!--Main-->
        <data name="plink_out" format="pbed"/>

        <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/>

        <!--Data Manage-->
        <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'>
            <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
        </data>
        <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'>
            <filter>functions['func'] == 'data_manage' and functions['recode']</filter>
        </data>

        <!--Stats-->
        <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'>
            <filter>functions['func'] == 'stats' and functions['freq']</filter>
        </data>
        <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'>
            <filter>functions['func'] == 'stats' and functions['hardy']</filter>
        </data>
        <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'>
            <filter>functions['func'] == 'stats' and functions['missing']</filter>
        </data>
        <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'>
            <filter>functions['func'] == 'stats' and functions['missing']</filter>
        </data>
        <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'>
            <filter>functions['func'] == 'stats' and functions['het']</filter>
        </data>
        <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'>
            <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
        </data>
        
        <!--Association-->
            <!--Assoc -->

        <data name='eigenvals' format='txt' from_work_dir='plink_output/plink_output.mds.eigvals' label='${tool.name}: Eigenvals'>
            <filter>functions['func'] == 'stratification' and functions['cluster']['cluster'] == 'Yes' and functions['cluster']['mds']['mds_scaling'] == 'Yes' and functions['cluster']['mds']['modifiers'] and 'eigvals' in functions['cluster']['mds']['modifiers']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs='2'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='filtering'/>
                <conditional name='id_list'>

                    <param name='sex_select' value='--filter-cases'/>
                    <param name='no_sex_select' value='--allow-no-sex'/>
                    <param name='nonfounders' value='--nonfounders'/>
                </conditional>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/>
            </output>
            <expand macro="log_out_assert"/>
        </test>

        <test expect_num_outputs='4'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='data_manage'/>
                <conditional name='bmerge'>
                    <param name='set' value='Yes'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink_2.bim"/>
                        <composite_data value="plink_2.bed"/>
                        <composite_data value="plink_2.fam"/>
                    </param>
                </conditional>
                <param name='recode' value='--recode'/>
                <param name='template' value='@asd#123'/>
                <param name='length' value='23'/>
                <conditional name='update_cols'>

                    <param name='col_num' value='1'/>
                    <param name='var_col' value='2'/>
                    <param name='skip' value='a'/>
                </conditional>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/>
            </output>
            <expand macro="log_out_assert"/>
            <output name='plink_ped' file='out.ped'/>
            <output name='plink_map' file='out.map'/>
        </test>

        <test expect_num_outputs='2'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='vcf'/>
                    <param name='input' value='test.vcf'/>
                </conditional>
            </section>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/>
            </output>
            <expand macro="log_out_assert"/>
        </test>

        <test expect_num_outputs='8'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="x_plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='stats'/>
                <param name='freq' value='--freq'/>

                        <param name='female_max_obvs' value='10'/>
                        <param name='male_min_obvs' value='200'/>
                    </conditional>
                </conditional>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/>
            </output>
            <expand macro="log_out_assert"/>
            <output name='frequency' file='out.freq'/>
            <output name='hardy_out' file='out.hardy'/>
            <output name='missing_1' file='out.imiss'/>
            <output name='missing_2' file='out.lmiss'/>
            <output name='het' file='out.het'/>
            <output name='sex_check' file='out.sexcheck'/>
        </test>

        <test expect_num_outputs='4'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='link'/>
                <conditional name='set_indep'>

                    <param name='window' value='51'/>
                    <param name='step' value='6'/>
                    <param name='r2' value='0.3'/>
                </conditional>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/>
            </output>
            <expand macro="log_out_assert"/>
            <output name='prune_in' file='plink.prune.in'/>
        </test>
        
        <test expect_num_outputs='7'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='stratification'/>
                <param name='read_genome' value='plink.genome'/>

                        <param name='dimensions' value='10'/>
                        <param name='modifiers' value='eigendecomp,eigvals'/>
                    </conditional>
                </conditional>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/>
            </output>
            <expand macro="log_out_assert"/>
            <output name='mds' value='plink.mds' compare='sim_size'/>
            <output name='cluster1' value='plink.cluster1' compare='sim_size'/>
            <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
            <output name='cluster3' value='plink.cluster3' compare='sim_size'/>
            <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
        </test>

        <test expect_num_outputs='5'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='association'/>
                <conditional name='assoc'>

                    <param name='beta' value='beta'/>
                    <param name='intercept' value='intercept'/>
                </conditional>
                <param name='lambda' value='1.0'/>
            </conditional>
            <output name="plink_out">
                <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/>
                <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/>
                <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/>
            </output>
            <expand macro="log_out_assert"/>
            <output_collection name='assoc_outfiles'  type='list' count='2'>
                <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
                <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
            </output_collection>
            <output_collection name='adjust_outfiles' type='list' count='1'>

                <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/>
                <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/>
            </output_collection>
        </test>

        <test expect_num_outputs='3'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='' ftype="pbed">
                        <composite_data value="plink.bim"/>
                        <composite_data value="plink.bed"/>
                        <composite_data value="plink.fam"/>
                    </param>
                </conditional>
            </section>
            <conditional name='functions'>
                <param name='func' value='ibd'/>
                <conditional name='genome'>

                    <param name='min' value='0.1'/>
                    <param name='max' value='0.9'/>
                    <param name='modifiers' value='full,unbounded,nudge'/>
                </conditional>
            </conditional>
            <expand macro="log_out_assert"/>
            <output name='genome' file='out.genome'/>
        </test>
    </tests>
    <help><![CDATA[
        PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.