comparison plink.xml @ 8:16d22eee0fe3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"

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='@' />

                    <add value=' '/>
                </valid>
            </sanitizer>
        </xml>
    </macros>
    <requirements>
        <requirement type='package' version='1.90b6.18'>plink</requirement>
    </requirements>
    <command detect_errors='exit_code'><![CDATA[

            $functions.logistic.sex_covar
            $functions.logistic.interaction
            $functions.logistic.beta
            $functions.logistic.intercept
        #end if

    #elif $functions.func == 'ibd':
        #if $functions.genome.output_genome:
            --genome
            #for $type in $functions.genome.modifiers
                $type

                <!-- <option value='rerun'>Rerun</option> -->
            </param>
            <when value='filtering'>
                <conditional name='id_list'>
                    <param name='func' type='select' label='ID list functions'>
                        <option value='none'/>
                        <option value='keep'/>
                        <option value='keep-fam'/>
                        <option value='remove'/>
                        <option value='remove-fam'/>
                    </param>
                    <when value='none'/>
                    <when value='keep'>
                        <param format='tabular,tsv' name='file' type='data' label='Keep file.' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis;'/>
                    </when>

                        <param format='tabular,tsv' name='file' type='data' label='Remove-fam file' help='Acceptz text files with family IDs in the first column, and removes entire families.'/>
                    </when>
                </conditional>
                <conditional name='extraction'>
                    <param name='ex_func' type='select' label='ID extraction functions'>
                        <option value='none'/>
                        <option value='extract'/>
                        <option value='exclude'/>
                    </param>
                    <when value='none'/>
                    <when value='extract'>
                        <param format='txt' name='file' type='data' label='Extract' help='Accepts one or more text file(s) with variant IDs , and removes all unlisted variants from the current analysis'/>
                        <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/>

                        </param>
                    </when>
                </conditional>
                <conditional name='thinning'>
                    <param name='thinning' type='select' label='Arbitrary thinning'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='thin' type='float' label='Thin' min='0' max='1.0' help='Removes variants at random by retaining each variant with probability p' optional='true'/>
                        <param name='thin_count' type='integer' label='Thin Count' help='Removes variants at random until only n remain' min='1' optional='true'/>

                    <param name='mac' type='integer' label='Minimum allele count' min='1' help='Filters out all variants with allele counts below the provided threshold' optional='true'/>
                    <param name='max_mac' type='integer' label='Maximum allele count' min='0' help='filters out all variants with allele counts above the provided threshold' optional='true'/>
                </section>
                <conditional name='hwe'>
                    <param  name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='hwe_val' type='float' label='Hardy-Weinberg Equilibrium' help='Filters out all variants which have Hardy-Weinberg equilibrium exact test 
                        p-value below the provided threshold. It is recommended setting a low threshold—serious genotyping errors often yield extreme p-values like 1e-501 which 

                        </param>
                    </when>
                </conditional>
                <conditional name='sex_founder_filter'>
                    <param name='filter' type='select' label='Filter on sex and/or founders'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
                            <option value=''>Do not specifically filter out based on sex or founders</option>

                </conditional>
            </when>
            <when value='data_manage'>
                <conditional name='bmerge'>
                    <param name='set' type='select' label='Merge plink tilesets'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </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'/>

            </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'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='modifiers' type='select' label='Cluster flag modifiers' multiple='true' display='checkboxes' optional='true'>
                            <option value='cc'>Prevent two all-case or two all-control clusters from being merged.</option>
                            <option value='group-avg'>By default, the distance between two clusters is defined as the maximum pairwise distance between a member of the first cluster and a member of the second cluster. Cause average pairwise distance to be used instead.</option>
                            <option value='missing'>Cause clustering to be based on identity-by-missingness</option>
                        </param>
                        <conditional name='mds'>
                            <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
                                <option value='No'/>
                                <option value='Yes'/>
                            </param>
                            <when value='No'/>
                            <when value='Yes'>
                                <param name='dimensions' type='integer' label='Dimension count' value='10'/>
                                <param name='modifiers' type='select' label='mds-plot flag modifiers' multiple='true' display='checkboxes' optional='true'>

            </when>
            <when value='association'>
                <conditional name='assoc'>
                    <param name='assoc' label='Perform 1df chi-square allelic test' type='select'>
                        <option value=''>No</option>
                        <option value='Yes'/>
                    </param>
                    <when value=''/>
                    <when value='Yes'>
                        <conditional name='perm'>
                            <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>

                        <param name='count' label='Counts' type='boolean' truevalue='counts' falsevalue='' checked='false' help='Report allele counts instead of frequencies'/>
                    </when>
                </conditional>
                <conditional name='adjust'>
                    <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='tests' label='Testing modifiers' type='select' multiple='true' display='checkboxes' optional='true'>
                            <option value='gc'>Use genomic-controlled p-values in the formulas</option>

                        <param name='intercept' label='intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/>
                    </when>
                </conditional> -->
                <conditional name='logistic'>
                    <param name='logistic' type='select' label='Perform logistic regression and return report'>
                        <option value='No'/>
                        <option value='Yes'/>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <conditional name='perm'>
                            <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>

            </when> -->
            <when value='ibd'>
                <conditional name='genome'>
                    <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'>
                        <option value=''>No</option>
                        <option value='Yes'/>
                    </param>
                    <when value=''/>
                    <when value='Yes'>
                        <param name='min' type='float' label='min' min='0' max='1.0' help='Minimum PI_HAT value' optional='true'/>
                        <param name='max' type='float' label='max' min='0' max='1.0' help='Maximum PI_HAT value' optional='true'/>

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='@' />

                    <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[

            $functions.logistic.sex_covar
            $functions.logistic.interaction
            $functions.logistic.beta
            $functions.logistic.intercept
        #end if
        --lambda $functions.lambda
    #elif $functions.func == 'ibd':
        #if $functions.genome.output_genome:
            --genome
            #for $type in $functions.genome.modifiers
                $type

                <!-- <option value='rerun'>Rerun</option> -->
            </param>
            <when value='filtering'>
                <conditional name='id_list'>
                    <param name='func' type='select' label='ID list functions'>
                        <option value='none'>None</option>
                        <option value='keep'>Keep by sample IDs</option>
                        <option value='keep-fam'>Keep by family IDs</option>
                        <option value='remove'>Remove by sample IDs</option>
                        <option value='remove-fam'>Remove by family IDs</option>
                    </param>
                    <when value='none'/>
                    <when value='keep'>
                        <param format='tabular,tsv' name='file' type='data' label='Keep file.' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis;'/>
                    </when>

                        <param format='tabular,tsv' name='file' type='data' label='Remove-fam file' help='Acceptz text files with family IDs in the first column, and removes entire families.'/>
                    </when>
                </conditional>
                <conditional name='extraction'>
                    <param name='ex_func' type='select' label='ID extraction functions'>
                        <option value='none'>None</option>
                        <option value='extract'>Keep by variant IDs</option>
                        <option value='exclude'>Remove by variant IDs </option>
                    </param>
                    <when value='none'/>
                    <when value='extract'>
                        <param format='txt' name='file' type='data' label='Extract' help='Accepts one or more text file(s) with variant IDs , and removes all unlisted variants from the current analysis'/>
                        <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/>

                        </param>
                    </when>
                </conditional>
                <conditional name='thinning'>
                    <param name='thinning' type='select' label='Arbitrary thinning'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='thin' type='float' label='Thin' min='0' max='1.0' help='Removes variants at random by retaining each variant with probability p' optional='true'/>
                        <param name='thin_count' type='integer' label='Thin Count' help='Removes variants at random until only n remain' min='1' optional='true'/>

                    <param name='mac' type='integer' label='Minimum allele count' min='1' help='Filters out all variants with allele counts below the provided threshold' optional='true'/>
                    <param name='max_mac' type='integer' label='Maximum allele count' min='0' help='filters out all variants with allele counts above the provided threshold' optional='true'/>
                </section>
                <conditional name='hwe'>
                    <param  name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='hwe_val' type='float' label='Hardy-Weinberg Equilibrium' help='Filters out all variants which have Hardy-Weinberg equilibrium exact test 
                        p-value below the provided threshold. It is recommended setting a low threshold—serious genotyping errors often yield extreme p-values like 1e-501 which 

                        </param>
                    </when>
                </conditional>
                <conditional name='sex_founder_filter'>
                    <param name='filter' type='select' label='Filter on sex and/or founders'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
                            <option value=''>Do not specifically filter out based on sex or founders</option>

                </conditional>
            </when>
            <when value='data_manage'>
                <conditional name='bmerge'>
                    <param name='set' type='select' label='Merge plink tilesets'>
                        <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'/>

            </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'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='modifiers' type='select' label='Cluster flag modifiers' multiple='true' display='checkboxes' optional='true'>
                            <option value='cc'>Prevent two all-case or two all-control clusters from being merged.</option>
                            <option value='group-avg'>By default, the distance between two clusters is defined as the maximum pairwise distance between a member of the first cluster and a member of the second cluster. Cause average pairwise distance to be used instead.</option>
                            <option value='missing'>Cause clustering to be based on identity-by-missingness</option>
                        </param>
                        <conditional name='mds'>
                            <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
                                <option value='No'>No</option>
                                <option value='Yes'>Yes</option>
                            </param>
                            <when value='No'/>
                            <when value='Yes'>
                                <param name='dimensions' type='integer' label='Dimension count' value='10'/>
                                <param name='modifiers' type='select' label='mds-plot flag modifiers' multiple='true' display='checkboxes' optional='true'>

            </when>
            <when value='association'>
                <conditional name='assoc'>
                    <param name='assoc' label='Perform 1df chi-square allelic test' type='select'>
                        <option value=''>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value=''/>
                    <when value='Yes'>
                        <conditional name='perm'>
                            <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>

                        <param name='count' label='Counts' type='boolean' truevalue='counts' falsevalue='' checked='false' help='Report allele counts instead of frequencies'/>
                    </when>
                </conditional>
                <conditional name='adjust'>
                    <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <param name='tests' label='Testing modifiers' type='select' multiple='true' display='checkboxes' optional='true'>
                            <option value='gc'>Use genomic-controlled p-values in the formulas</option>

                        <param name='intercept' label='intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/>
                    </when>
                </conditional> -->
                <conditional name='logistic'>
                    <param name='logistic' type='select' label='Perform logistic regression and return report'>
                        <option value='No'>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value='No'/>
                    <when value='Yes'>
                        <conditional name='perm'>
                            <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>

            </when> -->
            <when value='ibd'>
                <conditional name='genome'>
                    <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'>
                        <option value=''>No</option>
                        <option value='Yes'>Yes</option>
                    </param>
                    <when value=''/>
                    <when value='Yes'>
                        <param name='min' type='float' label='min' min='0' max='1.0' help='Minimum PI_HAT value' optional='true'/>
                        <param name='max' type='float' label='max' min='0' max='1.0' help='Maximum PI_HAT value' optional='true'/>