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comparison StatSTR/statSTR.xml @ 1:8e8cf43f6836 draft default tip

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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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0:ecf8c4f9f8ba 1:8e8cf43f6836
175 </outputs> 175 </outputs>
176 176
177 177
178 <tests> 178 <tests>
179 <test> 179 <test>
180 <section name="main_params"> 180 <section name="input_output">
181 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> 181 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
182 <param name="out" value="test_result"/> 182 <param name="out" value="test_result"/>
183 <param name="vcftype" value="hipstr"/> 183 <param name="vcftype" value="hipstr"/>
184 </section>
185 <section name="opt_basic">
186 <param name="precision" value="5"/> 184 <param name="precision" value="5"/>
187 </section> 185 </section>
188 <section name="statistic_opt"> 186
187 <section name="stats_group">
189 <param name="thresh" value="true"/> 188 <param name="thresh" value="true"/>
190 <param name="afreq" value="true"/> 189 <param name="afreq" value="true"/>
191 <param name="acount" value="true"/> 190 <param name="acount" value="true"/>
192 <param name="hwep" value="true"/> 191 <param name="hwep" value="true"/>
193 <param name="het" value="true"/> 192 <param name="het" value="true"/>
209 208
210 </test> 209 </test>
211 </tests> 210 </tests>
212 211
213 212
214 <help>usage: main.py [-h] --vcf VCF --out OUT [--vcftype VCFTYPE] [--precision PRECISION] [--samples SAMPLES] 213 <help>usage: pygalgen [-h] --vcf VCF --out OUT [--vcftype VCFTYPE] [--precision PRECISION] [--samples SAMPLES]
215 [--sample-prefixes SAMPLE_PREFIXES] [--region REGION] [--thresh] [--afreq] [--acount] [--hwep] [--het] 214 [--sample-prefixes SAMPLE_PREFIXES] [--region REGION] [--thresh] [--afreq] [--acount] [--hwep] [--het]
216 [--entropy] [--mean] 215 [--entropy] [--mean] [--mode] [--var] [--numcalled] [--use-length] [--plot-afreq] [--version]
217 [--mode] [--var] [--numcalled] [--use-length] [--plot-afreq] [--version] 216
218 217 options:
219 options: 218 -h, --help show this help message and exit
220 -h, --help show this help message and exit 219
221 220 Input/output:
222 Input/output: 221 --vcf VCF Input STR VCF file
223 --vcf VCF Input STR VCF file 222 --out OUT Output file prefix. Use stdout to print file to standard output. In addition, if not stdout
224 --out OUT Output file prefix. Use stdout to print file to standard output. In addition, if not stdout then 223 then timing diagnostics are print to stdout.
225 timing diagnostics are print to stdout. 224 --vcftype VCFTYPE Genotyper that created the VCF file
226 --vcftype VCFTYPE ##!!## Name trh could not be loaded 225 --precision PRECISION
227 --precision PRECISION 226 How much precision to use when printing decimals
228 How much precision to use when printing decimals 227
229 228 Filtering group:
230 Filtering group: 229 --samples SAMPLES File containing list of samples to include. Or a comma-separated list of files to compute
231 --samples SAMPLES File containing list of samples to include. Or a comma-separated list of files to compute 230 stats separate for each group of samples
232 stats separate for each group of samples 231 --sample-prefixes SAMPLE_PREFIXES
233 --sample-prefixes SAMPLE_PREFIXES 232 Prefixes to name output for each samples group. By default uses 1,2,3 etc.
234 Prefixes to name output for each samples group. By default uses 1,2,3 etc. 233 --region REGION Restrict to the region chrom:start-end. Requires file to bgzipped and tabix indexed.
235 --region REGION Restrict to the region chrom:start-end. Requires file to bgzipped and tabix indexed. 234
236 235 Stats group:
237 Stats group: 236 --thresh Output threshold field (max allele size, used for GangSTR strinfo).
238 --thresh Output threshold field (max allele size, used for GangSTR strinfo). 237 --afreq Output allele frequencies
239 --afreq Output allele frequencies 238 --acount Output allele counts
240 --acount Output allele counts 239 --hwep Output HWE p-values per loci.
241 --hwep Output HWE p-values per loci. 240 --het Output the heterozygosity of each locus.
242 --het Output the heterozygosity of each locus. 241 --entropy Output the entropy of each locus.
243 --entropy Output the entropy of each locus. 242 --mean Output mean of the allele frequencies.
244 --mean Output mean of the allele frequencies. 243 --mode Output mode of the allele frequencies.
245 --mode Output mode of the allele frequencies. 244 --var Output variance of the allele frequencies.
246 --var Output variance of the allele frequencies. 245 --numcalled Output number of samples called.
247 --numcalled Output number of samples called. 246 --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length. This is implicitly true for
248 --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length. This is implicitly true for 247 genotypers which only emit length based genotypes.
249 genotypers which only emit length based genotypes. 248
250 249 Plotting group:
251 Plotting group: 250 --plot-afreq Output allele frequency plot. Will only do for a maximum of 10 TRs.
252 --plot-afreq Output allele frequency plot. Will only do for a maximum of 10 TRs. 251
253 252 Version:
254 Version: 253 --version show program's version number and exit
255 --version show program's version number and exit
256 </help> 254 </help>
257 255
258 256
259 <citations> 257 <citations>
260 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats, 258 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,