Mercurial > repos > iuc > king
changeset 0:ec2bc87ebd7b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a"
| author | iuc |
|---|---|
| date | Tue, 16 Nov 2021 20:14:31 +0000 |
| parents | |
| children | 1932808c6fab |
| files | king.xml test-data/new.6000.bed test-data/new.6000.bim test-data/new.6000.fam test-data/new.6000.log |
| diffstat | 5 files changed, 6676 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/king.xml Tue Nov 16 20:14:31 2021 +0000 @@ -0,0 +1,328 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="king" name="KING" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Kinship-based INference for GWAS</description> + <macros> + <token name="@TOOL_VERSION@">2.2.4</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">king</requirement> + <requirement type="package" version="1.6.4">r-kinship2</requirement> + <requirement type="package" version="1.2.2">r-igraph</requirement> + </requirements> + <version_command> + king | head -1 | cut -d' ' -f 2 + </version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$genotype' input.bed && + ln -s '$family' input.fam && + ln -s '$map' input.bim && + + king -b input.bed --fam input.fam --bim input.bim + $related + $duplicate + $kinship + $ibdseg + $ibs + $homog + #if str($degree): + --degree $degree + #end if + #if str($projection): + --projection $projection + #end if + $unrelated + $build + $cluster + $rplot + + > '$kingoutlog' + ]]></command> + <inputs> + <param name="genotype" type="data" format="pbed,binary" label="Binary Genotype File" /> + <param name="family" type="data" format="lped,txt" label="Family File" /> + <param name="map" type="data" format="tabular" label="Map File" /> + <!-- Beginning of the optional paramters --> + <param argument="--related" type="boolean" truevalue="--related" falsevalue="" label="Relationship Inference" help="Implements the fastest and integrated relationship inference." /> + <param argument="--duplicate" type="boolean" truevalue="--duplicate" falsevalue="" label="Duplicate Analysis" help="Implements the fastest (and accurate) algorithm to identify duplicates or MZ twins" /> + <param argument="--kinship" type="boolean" truevalue="--kinship" falsevalue="" label="Kinship Inference" help="Estimates pair-wise kinship coefficients" /> + <param argument="--ibdseg" type="boolean" truevalue="--ibdseg" falsevalue="" label="IBD Segment Analysis" help="IBD segment analysis determines all IBD (IBD1 and IBD2) segments shared between relatives" /> + <param argument="--ibs" type="boolean" truevalue="--ibs" falsevalue="" label="IBS Summary Statistics" help="Counts and average of IBS" /> + <param argument="--homog" type="boolean" truevalue="--homog" falsevalue="" label="Homogeneous Population" help="Estimates pair-wise kinship coefficients assuming a homogeneous population." /> + <param argument="--degree" type="integer" min="0" optional="true" label="Degrees of relatedness" help="Filters relative pairs based on kinship coefficients." /> + <param argument="--projection" type="integer" min="0" optional="true" label="Projection N" help="Includes the first N samples of a subset." /> + <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue="" label="Unrelated Option" help="Extract a list of unrelated individuals." /> + <param argument="--build" type="boolean" truevalue="--build" falsevalue="" label="Reconstruct Pedigree" help="Reconstructs pedigrees using SNP data" /> + <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" label="Cluster Parameter" help="Clusters relatives into families by generating an updateid file." /> + <param argument="--rplot" type="boolean" truevalue="--rplot" falsevalue="" label="R Code and Plots" help="Generates R code first and then calls R program to make plots in a PDF file." /> + <param name="use_log" type="boolean" checked="false" label="Output a Log?" /> + </inputs> + <outputs> + <data name="kingoutlog" format="txt" label="${tool.name} on ${on_string} : Log" > + <filter>use_log == True</filter> + </data> + <collection name="kingoutput_txt" type="list" label="${tool.name} on ${on_string}: Metrics"> + <discover_datasets pattern="king(?P<designation>.+)\.txt" format="txt" /> + </collection> + <collection name="kingoutput_log" type="list" label="${tool.name} on ${on_string}: Metrics Logs" > + <filter>use_log == True</filter> + <discover_datasets pattern="king(?P<designation>.+)\.log" format="txt" /> + </collection> + <collection name="kingoutput_pdf" type="list" label="${tool.name} on ${on_string}: Plots"> + <discover_datasets pattern="king_(?P<designation>.+)\.pdf" format="pdf" /> + </collection> + </outputs> + <tests> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="related" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/> + <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" /> + <has_text text="--related" /> + <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="related" value="true" /> + <param name="degree" value="2" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is"/> + <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" /> + <has_text text="--related" /> + <has_text text="--degree 2" /> + <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="related" value="true" /> + <param name="degree" value="2" /> + <param name="rplot" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + <has_text text="--related" /> + <has_text text="--degree 2" /> + <has_text text="--rplot" /> + <has_text text="(with 6000 SNPs): 8 pairs of relatives are detected (with kinship > 0.0625)" /> + <has_text text="Relationship summary (total relatives: 0 by pedigree, 6 by inference)" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="duplicate" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/> + <has_text text="--duplicate" /> + <has_text text="No duplicates are found with heterozygote concordance rate > 80%." /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="kinship" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/> + <has_text text="--kinship" /> + <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="related" value="true" /> + <param name="projection" value="100000" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals."/> + <has_text text="--related" /> + <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" /> + <has_text text="PLINK pedigrees loaded: 332 samples" /> + <has_text text="PLINK maps loaded: 6000 SNPs" /> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="ibdseg" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="--ibdseg" /> + <has_text text="Sample pairs without any long IBD segments (>10Mb) are excluded." /> + <has_text text="IBD segments saved in a gzipped file king.segments.gz" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="ibdseg" value="true" /> + <param name="degree" value="3" /> + <param name="rplot" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="--ibdseg" /> + <has_text text="--rplot" /> + <has_text text="--degree 3" /> + <has_text text="Summary statistics of IBD segments for individual pairs saved in file king.seg" /> + <has_text text="Genotype data consist of 6000 autosome SNPs" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="ibs" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." /> + <has_text text="Within-family IBS data saved in file king.ibs" /> + <has_text text="--ibs" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + <has_text text="Information of these chromosomal segments can be found in file kingallsegs.txt" /> + <has_text text="Between-family IBS data saved in file king.ibs0" /> + <has_text text="Relationship summary (total relatives: 200 by pedigree, 200 by inference)" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="homog" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="Autosome genotypes stored in 375 words for each of 332 individuals." /> + <has_text text="--homo" /> + <has_text text="Within-family kinship data saved in file king.kin" /> + <has_text text="Genotype data consist of 6000 autosome SNPs" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="unrelated" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="--unrelated" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + <has_text text="Y028,Y117" /> + <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="unrelated" value="true" /> + <param name="degree" value="2" /> + <param name="use_log" value="true" /> + <output name="kingoutlog" > + <assert_contents> + <has_text text="--unrelated" /> + <has_text text="--degree 2" /> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." /> + <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="build" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog" > + <assert_contents> + <has_text text="--build" /> + <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." /> + <has_text text="Update-ID information is saved in file kingupdateids.txt" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="build" value="true" /> + <param name="degree" value="2" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="--build" /> + <has_text text="--degree 2" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + <has_text text="Update-parent information is saved in file kingupdateparents.txt" /> + </assert_contents> + </output> + </test> + <test> + <param name="genotype" value="new.6000.bed"/> + <param name="family" value="new.6000.fam"/> + <param name="map" value="new.6000.bim"/> + <param name="cluster" value="true" /> + <param name="use_log" value="true" /> + <output name="kingoutlog"> + <assert_contents> + <has_text text="--cluster" /> + <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" /> + <has_text text="Pair-wise relatedness in newly clustered families saved in kingcluster.kin." /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + + `KING <http://people.virginia.edu/~wc9c/KING/>`_ is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) + or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, + quality control, population substructure identification, forensics, gene mapping, etc. + + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btq559</citation> + </citations> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/new.6000.log Tue Nov 16 20:14:31 2021 +0000 @@ -0,0 +1,16 @@ +PLINK v1.90b6.21 64-bit (19 Oct 2020) +Options in effect: + --file sub + --out new.6000 + +Hostname: kaktus +Working directory: /home/tetris/repos/_galaxy/tools-iuc/tools/king/test-data +Start time: Wed Oct 20 16:14:42 2021 + +Random number seed: 1634739282 +15797 MB RAM detected; reserving 7898 MB for main workspace. +Scanning .ped file... done. +Performing single-pass .bed write (6000 variants, 332 people). +--file: new.6000.bed + new.6000.bim + new.6000.fam written. + +End time: Wed Oct 20 16:14:42 2021