comparison plink.xml @ 7:66b35562554d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"

6:f76d842e960f

<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
    <macros>
        <token name='@TOOL_VERSION@'>1.9.b618</token>
        <token name='@VERSION_SUFFIX@'>1</token>
        <xml name='template_sanitizer'>
            <sanitizer>
                <valid initial='default'>
                    <add value='#' />
                    <add value='@' />

    ## Plink commands by section
    #if $inputs.covar_input:
            --covar '$inputs.covar_input'
    #end if
    #if $inputs.pheno:
        --pheno $inputs.pheno
    #end if
    #if $functions.func == 'filtering':
        ##ID list functions
            #if $functions.id_list.func == 'keep':
                --keep '$functions.id_list.file'

##      
    #end if
    --memory \${GALAXY_MEMORY_MB:-8192}
    --make-bed
    --out plink_output/plink_output
    ]]></command>
    <inputs>
        <section name='inputs' title='Data inputs' expanded='true'>
            <conditional name='inputs'>
                <param name='filetype' type='select' label='Main input data type'>

                </when>
                <when value='vcf'>
                    <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
                </when>
            </conditional>
            <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/> 
            <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>
        </section>
        <conditional name='functions'>
            <param name='func' type='select' label='Plink functions'>
                <option value='filtering'>Filtering</option>

        <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='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter>         
        </data>
        <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter>
        </data>
        <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association Max(T) permutation test'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and not functions['assoc']['fisher']</filter>
        </data>
        <data name='fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher' label='${tool.name}: Association Fisher'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['fisher']</filter>
        </data>
        <data name='fisher_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.perm' label='${tool.name}: Association Fisher perm'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and functions['assoc']['fisher']</filter>
        </data>
        <data name='fisher_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.mperm' label='${tool.name}: Association Fisher mperm'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and functions['assoc']['fisher']</filter>
        </data>

           <!--adjust-->
        <data name='adjust' format='tabular' from_work_dir='plink_output/plink_output.assoc.adjusted' label='${tool.name}: Adjusted'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and not functions['assoc']['fisher']</filter>
        </data>
        <data name='adjust_fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.adjusted' label='${tool.name}: Fisher Adjusted'>
            <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and functions['assoc']['fisher']</filter>
        </data>
        <data name='adjust_logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.adjusted' label='${tool.name}: Logistic Adjusted'>
            <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes' and functions['logistic']['logistic'] == 'Yes'</filter>
        </data>

        <!-- <data name='linear' format='tabular' from_work_dir='plink_output/plink_output.assoc.linenar' label='${tool.name}: Linear Regression'>
            <filter>functions['func'] == 'association' and functions.func.association.linear['linear'] == 'Yes'</filter>
        </data> -->

            <!--Logistic-->
        <data name='logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic' label='${tool.name}: Logistic Regression'>
            <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter>
        </data>
        <data name='logistic_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.perm' label='${tool.name}: Logistic Association Monte Carlo'>
            <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and  functions['logistic']['perm']['perm'] == 'perm'</filter>
        </data>
        <data name='logistic_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.mperm' label='${tool.name}: Logistic Association Max(T) permutation test'>
            <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and  functions['logistic']['perm']['perm'] == 'mperm'</filter>
        </data>
        
        <!--Link-->
        <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'>
            <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
        </data>
        <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'>

            <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='11'>
            <section name='inputs'>
                <conditional name='inputs'>
                    <param name='filetype' value='bfile'/>
                    <param name='bed' value='plink.bed'/>
                    <param name='bim' value='plink.bim'/>

            <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 name='fisher' value="out.assoc.fisher"/>
            <output name='adjust_fisher' value="out.assoc.fisher.adjusted" sort="True" />
            <output name='fisher_mperm' value="out.assoc.fisher.mperm" compare='sim_size'/>
            <output name='logistic' value="out.assoc.logistic"/>
            <output name='adjust_logistic' value="out.assoc.logistic.adjusted"/>
            <output name='logistic_perm' value="out.assoc.logistic.perm" compare='sim_size'/>
        </test>

        <test expect_num_outputs='6'>
            <section name='inputs'>
                <conditional name='inputs'>

7:66b35562554d

<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
    <macros>
        <token name='@TOOL_VERSION@'>1.9.b618</token>
        <token name='@VERSION_SUFFIX@'>2</token>
        <xml name='template_sanitizer'>
            <sanitizer>
                <valid initial='default'>
                    <add value='#' />
                    <add value='@' />

    ## Plink commands by section
    #if $inputs.covar_input:
            --covar '$inputs.covar_input'
    #end if
    #if $inputs.set_pheno.set_pheno == 'Yes':
        --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno
    #end if
    #if $functions.func == 'filtering':
        ##ID list functions
            #if $functions.id_list.func == 'keep':
                --keep '$functions.id_list.file'

##      
    #end if
    --memory \${GALAXY_MEMORY_MB:-8192}
    --make-bed
    --out plink_output/plink_output

    #if $functions.func == 'association':
        #if $functions.logistic.logistic == 'Yes':
            && mkdir logistic_out
            && mv plink_output/plink_output.*.l* logistic_out
            && find ./logistic_out/. -type f -exec mv {} {}.txt ';'
        #end if
        #if $functions.adjust.adjust == 'Yes':
            && mkdir adjust_out
            && mv ./plink_output/*.adjuste* adjust_out
            && find ./adjust_out/. -type f -exec mv {} {}.txt ';'
        #end if
        #if $functions.assoc.assoc == 'Yes':
            && 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'>

                </when>
                <when value='vcf'>
                    <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
                </when>
            </conditional>
            <conditional name='set_pheno'>
                <param name='set_pheno' type='select' label='Set phenotype'>
                    <option value=''>No</option>
                    <option value='Yes'>Yes</option>
                </param>
                <when value=''/>
                <when value='Yes'>
                    <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.'/> 
                    <param name='all_pheno' type='boolean' truevalue='--all-pheno' falsevalue='' label='Allow all phenotypes present in the phenotype file to be subject to the association tests you have requested' checked='false'/>
                </when>
            </conditional>
            <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>
        </section>
        <conditional name='functions'>
            <param name='func' type='select' label='Plink functions'>
                <option value='filtering'>Filtering</option>

        <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 -->
        <collection name='assoc_outfiles' type='list' label='Association outfiles'>
            <discover_datasets directory='assoc_out' pattern='__name_and_ext__'/>
                <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes'</filter>
        </collection>
            <!--Adjust-->
        <collection name='adjust_outfiles' type='list' label='Adjust outfiles'>
            <discover_datasets directory='adjust_out' pattern='__name_and_ext__'/>
                <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes'</filter>
        </collection>
            <!--Logistic-->
        <collection name='log_outfiles' type='list' label='Logistic outfiles'>
            <discover_datasets directory='logistic_out' pattern='__name_and_ext__'/>
                <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter>
        </collection>   
        <!--Link-->
        <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'>
            <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
        </data>
        <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'>

            <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'/>

            <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.fisher.adjusted' value='out.assoc.fisher.adjusted' compare='sim_size' />
            </output_collection>
            <output_collection name='log_outfiles' type='list' count='3'>
                <element name='plink_output.assoc.logistic' value='out.assoc.logistic'/>
                <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'>