| Next changeset 1:1932808c6fab (2022-04-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/king/ commit 7e521e5df8cac36549fed2488034c9d1c4376a3a" |
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added:
king.xml test-data/new.6000.bed test-data/new.6000.bim test-data/new.6000.fam test-data/new.6000.log |
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| diff -r 000000000000 -r ec2bc87ebd7b king.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/king.xml Tue Nov 16 20:14:31 2021 +0000 |
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| b'@@ -0,0 +1,328 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<tool id="king" name="KING" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>Kinship-based INference for GWAS</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.2.4</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">king</requirement>\n+ <requirement type="package" version="1.6.4">r-kinship2</requirement>\n+ <requirement type="package" version="1.2.2">r-igraph</requirement>\n+ </requirements>\n+ <version_command>\n+ king | head -1 | cut -d\' \' -f 2\n+ </version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ln -s \'$genotype\' input.bed &&\n+ ln -s \'$family\' input.fam &&\n+ ln -s \'$map\' input.bim &&\n+\n+ king -b input.bed --fam input.fam --bim input.bim\n+ $related\n+ $duplicate\n+ $kinship\n+ $ibdseg\n+ $ibs\n+ $homog\n+ #if str($degree):\n+ --degree $degree\n+ #end if\n+ #if str($projection):\n+ --projection $projection\n+ #end if\n+ $unrelated\n+ $build\n+ $cluster\n+ $rplot\n+\n+ > \'$kingoutlog\'\n+ ]]></command>\n+ <inputs>\n+ <param name="genotype" type="data" format="pbed,binary" label="Binary Genotype File" />\n+ <param name="family" type="data" format="lped,txt" label="Family File" />\n+ <param name="map" type="data" format="tabular" label="Map File" />\n+ <!-- Beginning of the optional paramters -->\n+ <param argument="--related" type="boolean" truevalue="--related" falsevalue="" label="Relationship Inference" help="Implements the fastest and integrated relationship inference." />\n+ <param argument="--duplicate" type="boolean" truevalue="--duplicate" falsevalue="" label="Duplicate Analysis" help="Implements the fastest (and accurate) algorithm to identify duplicates or MZ twins" />\n+ <param argument="--kinship" type="boolean" truevalue="--kinship" falsevalue="" label="Kinship Inference" help="Estimates pair-wise kinship coefficients" />\n+ <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" />\n+ <param argument="--ibs" type="boolean" truevalue="--ibs" falsevalue="" label="IBS Summary Statistics" help="Counts and average of IBS" />\n+ <param argument="--homog" type="boolean" truevalue="--homog" falsevalue="" label="Homogeneous Population" help="Estimates pair-wise kinship coefficients assuming a homogeneous population." />\n+ <param argument="--degree" type="integer" min="0" optional="true" label="Degrees of relatedness" help="Filters relative pairs based on kinship coefficients." />\n+ <param argument="--projection" type="integer" min="0" optional="true" label="Projection N" help="Includes the first N samples of a subset." />\n+ <param argument="--unrelated" type="boolean" truevalue="--unrelated" falsevalue="" label="Unrelated Option" help="Extract a list of unrelated individuals." />\n+ <param argument="--build" type="boolean" truevalue="--build" falsevalue="" label="Reconstruct Pedigree" help="Reconstructs pedigrees using SNP data" />\n+ <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" label="Cluster Parameter" help="Clusters relatives into families by generating an updateid file." />\n+ <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." />\n+ <param name="use_log" type="boolean" checked="false" label="Output a Log?" />\n+ </inputs>\n+ <outputs>\n+ <data name="kingoutlog" format="txt" label="${tool.name} on ${on_string} : Log" >\n+ <filter>use_log == True</filter>\n+ </data>\n+ <collection name="kin'..b'" />\n+ <has_text text="Y028,Y117" />\n+ <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="genotype" value="new.6000.bed"/>\n+ <param name="family" value="new.6000.fam"/>\n+ <param name="map" value="new.6000.bim"/>\n+ <param name="unrelated" value="true" />\n+ <param name="degree" value="2" />\n+ <param name="use_log" value="true" />\n+ <output name="kingoutlog" >\n+ <assert_contents>\n+ <has_text text="--unrelated" />\n+ <has_text text="--degree 2" />\n+ <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />\n+ <has_text text="An alternative list of 114 to-be-removed individuals saved in file kingunrelated_toberemoved.txt" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="genotype" value="new.6000.bed"/>\n+ <param name="family" value="new.6000.fam"/>\n+ <param name="map" value="new.6000.bim"/>\n+ <param name="build" value="true" />\n+ <param name="use_log" value="true" />\n+ <output name="kingoutlog" >\n+ <assert_contents>\n+ <has_text text="--build" />\n+ <has_text text="Autosome genotypes stored in 94 words for each of 332 individuals." />\n+ <has_text text="Update-ID information is saved in file kingupdateids.txt" />\n+ <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="genotype" value="new.6000.bed"/>\n+ <param name="family" value="new.6000.fam"/>\n+ <param name="map" value="new.6000.bim"/>\n+ <param name="build" value="true" />\n+ <param name="degree" value="2" />\n+ <param name="use_log" value="true" />\n+ <output name="kingoutlog">\n+ <assert_contents>\n+ <has_text text="--build" />\n+ <has_text text="--degree 2" />\n+ <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />\n+ <has_text text="Update-parent information is saved in file kingupdateparents.txt" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="genotype" value="new.6000.bed"/>\n+ <param name="family" value="new.6000.fam"/>\n+ <param name="map" value="new.6000.bim"/>\n+ <param name="cluster" value="true" />\n+ <param name="use_log" value="true" />\n+ <output name="kingoutlog">\n+ <assert_contents>\n+ <has_text text="--cluster" />\n+ <has_text text="Total length of 6 chromosomal segments usable for IBD segment analysis is" />\n+ <has_text text="Pair-wise relatedness in newly clustered families saved in kingcluster.kin." />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+ `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)\n+ or a sequencing project. Applications of KING include family relationship inference and pedigree error checking,\n+ quality control, population substructure identification, forensics, gene mapping, etc.\n+\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btq559</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ec2bc87ebd7b test-data/new.6000.bed |
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| Binary file test-data/new.6000.bed has changed |
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| diff -r 000000000000 -r ec2bc87ebd7b test-data/new.6000.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/new.6000.bim Tue Nov 16 20:14:31 2021 +0000 |
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|
| b |
| diff -r 000000000000 -r ec2bc87ebd7b test-data/new.6000.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/new.6000.fam Tue Nov 16 20:14:31 2021 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r ec2bc87ebd7b test-data/new.6000.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/new.6000.log Tue Nov 16 20:14:31 2021 +0000 |
| b |
| @@ -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 |