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plink2.xml
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<tool id="plink2" name="PLINK Genetic Toolbox" version="0.1.0">
<requirements>
<requirement type="package" version="1.90-beta3.36">plink</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command><![CDATA[
plink
--input_type=$input_selection.input_type
#if str($input_selection.input_type)=="pedmap"
--ped=$input_selection.ped
--map=$input_selection.ped
#elif str($input_selection.input_type)=="lped"
--lped_path=$input_selection.file.extra_files_path
--lped_basefile=$input_selection.file.metadata.base_name
#elif str($input_selection.input_type)=="pbed"
--pbed_path=$input_selection.bfile.extra_files_path
--pbed_basefile=$input_selection.bfile.metadata.base_name
#elif str($input_selection.input_type)=="bbf"
--bed=$input_selection.bed
--bim=$input_selection.bim
--fam=$input_selection.fam
#elif str($input_selection.input_type)=="vcf"
--vcf=$input_selection.vcf
#end if
#if $mind
--mind=$mind
#end if
#if $geno
--geno=$geno
#end if
#if $maf
--maf=$maf
#end if
#if $maxmaf
--maxmaf=$maxmaf
#end if
]]></command>
<inputs>
<conditional name="input_selection">
<param name="input_type" type="select" label="Select input file type" help="">
<option value="pedmap">Pedigree and genetic map (--ped and --map)</option>
<option value="lped">Uncompressed data (--file)</option>
<option value="pbed">Compressed data (--bfile)</option>
<option value="bbf">Compressed data (--bed --bim and --fam)</option>
<option value="vcf">VCF file (--vcf)</option>
</param>
<when value="pedmap">
<param name="ped" type="data" format="ped" label="Pedigree file (--ped)" help="Pedigree file format" />
<param name="map" type="data" format="map" label="Genetic map (--map)" help="File with SNP info" />
</when>
<when value="lped">
<param name="file" type="data" format="lped" label="Uncompressed data (--file)" help="" />
</when>
<when value="pbed">
<param name="bfile" type="data" format="pbed" label="Compressed data (--bfile)" help="" />
</when>
<when value="bbf">
<param name="bed" type="data" format="bed" label="Binary pedigree file (--bed)" help="" />
<param name="bim" type="data" format="txt" label="Binary genetic map (--bim)" help="" />
<param name="fam" type="data" format="txt" label="Family file (--fam)" help="" />
</when>
<when value="vcf">
<param name="vcf" type="data" format="vcf" label="VCF file (--vcf)" help="" />
</when>
</conditional>
<param name="mind" type="float" value="" optional="true" label="Max missingness per individual" help="Max allowed missing rate in sample" />
<param name="geno" type="float" value="" optional="true" label="Max missingness per SNP" help="Max allowed missing rate in SNP" />
<param name="maf" type="float" value="" optional="true" label="Minor allele frequency threshold (lower)" help="Include only SNPs above this threshold" />
<param name="maxmaf" type="float" value="" optional="true" label="Minor allele frequency threshold (upper)" help="Include only SNPs below this threshold" />
</inputs>
<outputs>
</outputs>
<tests>
<!-- PLINK2 test -->
<test>
<param name="input-type" value="pedmap" />
<param name="ped" value="toy.ped" />
<param name="map" value="toy.map" />
<output name="bed" file="toy.bed" ftype="bed" />
<output name="bim" file="toy.bim" ftype="bim" />
<output name="fam" file="toy.fam" ftype="fam" />
</test>
</tests>
<help><![CDATA[
PLINK v1.90b3.36 64-bit (31 Mar 2016) https://www.cog-genomics.org/plink2
(C) 2005-2016 Shaun Purcell, Christopher Chang GNU General Public License v3
plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
plink --help {flag name(s)...}
Commands include --make-bed, --recode, --flip-scan, --merge-list,
--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
--meta-analysis, --epistasis, --fast-epistasis, and --score.
'plink --help | more' describes all functions (warning: long).
]]></help>
<citations>
<citation type="bibtex">
@misc{renameTODO,
author = {LastTODO, FirstTODO},
year = {TODO},
title = {TODO},
url = {https://www.cog-genomics.org/plink2},
}</citation>
</citations>
</tool>