Mercurial > repos > michal_klinka > trtools
diff StatSTR/statSTR.xml @ 1:8e8cf43f6836 draft default tip
planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390
author | michal_klinka |
---|---|
date | Sun, 15 May 2022 15:23:59 +0000 |
parents | ecf8c4f9f8ba |
children |
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--- a/StatSTR/statSTR.xml Sat Apr 23 16:34:03 2022 +0000 +++ b/StatSTR/statSTR.xml Sun May 15 15:23:59 2022 +0000 @@ -177,15 +177,14 @@ <tests> <test> - <section name="main_params"> + <section name="input_output"> <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> <param name="out" value="test_result"/> <param name="vcftype" value="hipstr"/> - </section> - <section name="opt_basic"> <param name="precision" value="5"/> </section> - <section name="statistic_opt"> + + <section name="stats_group"> <param name="thresh" value="true"/> <param name="afreq" value="true"/> <param name="acount" value="true"/> @@ -211,48 +210,47 @@ </tests> - <help>usage: main.py [-h] --vcf VCF --out OUT [--vcftype VCFTYPE] [--precision PRECISION] [--samples SAMPLES] - [--sample-prefixes SAMPLE_PREFIXES] [--region REGION] [--thresh] [--afreq] [--acount] [--hwep] [--het] - [--entropy] [--mean] - [--mode] [--var] [--numcalled] [--use-length] [--plot-afreq] [--version] + <help>usage: pygalgen [-h] --vcf VCF --out OUT [--vcftype VCFTYPE] [--precision PRECISION] [--samples SAMPLES] + [--sample-prefixes SAMPLE_PREFIXES] [--region REGION] [--thresh] [--afreq] [--acount] [--hwep] [--het] + [--entropy] [--mean] [--mode] [--var] [--numcalled] [--use-length] [--plot-afreq] [--version] - options: - -h, --help show this help message and exit +options: + -h, --help show this help message and exit - Input/output: - --vcf VCF Input STR VCF file - --out OUT Output file prefix. Use stdout to print file to standard output. In addition, if not stdout then - timing diagnostics are print to stdout. - --vcftype VCFTYPE ##!!## Name trh could not be loaded - --precision PRECISION - How much precision to use when printing decimals +Input/output: + --vcf VCF Input STR VCF file + --out OUT Output file prefix. Use stdout to print file to standard output. In addition, if not stdout + then timing diagnostics are print to stdout. + --vcftype VCFTYPE Genotyper that created the VCF file + --precision PRECISION + How much precision to use when printing decimals - Filtering group: - --samples SAMPLES File containing list of samples to include. Or a comma-separated list of files to compute - stats separate for each group of samples - --sample-prefixes SAMPLE_PREFIXES - Prefixes to name output for each samples group. By default uses 1,2,3 etc. - --region REGION Restrict to the region chrom:start-end. Requires file to bgzipped and tabix indexed. +Filtering group: + --samples SAMPLES File containing list of samples to include. Or a comma-separated list of files to compute + stats separate for each group of samples + --sample-prefixes SAMPLE_PREFIXES + Prefixes to name output for each samples group. By default uses 1,2,3 etc. + --region REGION Restrict to the region chrom:start-end. Requires file to bgzipped and tabix indexed. - Stats group: - --thresh Output threshold field (max allele size, used for GangSTR strinfo). - --afreq Output allele frequencies - --acount Output allele counts - --hwep Output HWE p-values per loci. - --het Output the heterozygosity of each locus. - --entropy Output the entropy of each locus. - --mean Output mean of the allele frequencies. - --mode Output mode of the allele frequencies. - --var Output variance of the allele frequencies. - --numcalled Output number of samples called. - --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length. This is implicitly true for - genotypers which only emit length based genotypes. +Stats group: + --thresh Output threshold field (max allele size, used for GangSTR strinfo). + --afreq Output allele frequencies + --acount Output allele counts + --hwep Output HWE p-values per loci. + --het Output the heterozygosity of each locus. + --entropy Output the entropy of each locus. + --mean Output mean of the allele frequencies. + --mode Output mode of the allele frequencies. + --var Output variance of the allele frequencies. + --numcalled Output number of samples called. + --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length. This is implicitly true for + genotypers which only emit length based genotypes. - Plotting group: - --plot-afreq Output allele frequency plot. Will only do for a maximum of 10 TRs. +Plotting group: + --plot-afreq Output allele frequency plot. Will only do for a maximum of 10 TRs. - Version: - --version show program's version number and exit +Version: + --version show program's version number and exit </help>