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comparison CompareSTR/compareSTR.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
1 <?xml version="1.0" ?>
2 <tool id="compareSTR" name="CompareSTR" version="@tool_version@"> 1 <tool id="compareSTR" name="CompareSTR" version="@tool_version@">
3 <description>CompareSTR compares different TR callsets generated on the same samples against the same reference 2 <description>CompareSTR compares different TR callsets generated on the same samples against the same reference
4 panel. CompareSTR outputs overall, per-locus, and per-sample concordance information. 3 panel. CompareSTR outputs overall, per-locus, and per-sample concordance information.
5 </description> 4 </description>
6 <macros> 5 <macros>
181 </outputs> 180 </outputs>
182 181
183 182
184 <tests> 183 <tests>
185 <test> 184 <test>
186 <section name="required"> 185 <section name="required_arguments">
187 <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> 186 <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
188 <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> 187 <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz" />
189 <param name="out" value="test_result"/> 188 <param name="out" value="test_result"/>
190 </section> 189 </section>
191 190
192 <section name="stratification"> 191 <section name="metrics_to_stratify_results">
193 <param name="stratify_fields" value="DP,Q"/> 192 <param name="stratify_fields" value="DP,Q"/>
194 <param name="stratify_binsizes" value="0:50:5,0:1:0.1"/> 193 <param name="stratify_binsizes" value="0:50:5,0:1:0.1"/>
195 <param name="stratify_file" value="0"/> 194 <param name="stratify_file" value="0"/>
196 </section> 195 </section>
197 <section name="other"> 196 <section name="optional_arguments">
198 <param name="verbose" value="true"/> 197 <param name="verbose" value="true"/>
199 <param name="vcftype1" value="hipstr"/> 198 <param name="vcftype1" value="hipstr"/>
200 <param name="vcftype2" value="hipstr"/> 199 <param name="vcftype2" value="hipstr"/>
201 </section> 200 </section>
202 201
228 </output_collection> 227 </output_collection>
229 </test> 228 </test>
230 </tests> 229 </tests>
231 230
232 231
233 <help>usage: main.py [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION] [--stratify-fields 232 <help>usage: pygalgen [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION]
234 STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES] [--stratify-file STRATIFY_FILE] [--period] 233 [--stratify-fields STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES]
235 [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX] [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1 234 [--stratify-file STRATIFY_FILE] [--period] [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX]
236 VCFTYPE1] [--vcftype2 VCFTYPE2] [--ignore-phasing] [--version] 235 [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1 VCFTYPE1] [--vcftype2 VCFTYPE2]
237 236 [--ignore-phasing] [--version]
238 options: 237
239 -h, --help show this help message and exit 238 options:
240 239 -h, --help show this help message and exit
241 Required arguments: 240
242 --vcf1 VCF1 First VCF file to compare (must be sorted, bgzipped, and indexed) 241 Required arguments:
243 --vcf2 VCF2 Second VCF file to compare (must be sorted, bgzipped, and indexed) 242 --vcf1 VCF1 First VCF file to compare (must be sorted, bgzipped, and indexed)
244 --out OUT Prefix to name output files 243 --vcf2 VCF2 Second VCF file to compare (must be sorted, bgzipped, and indexed)
245 244 --out OUT Prefix to name output files
246 Filtering options: 245
247 --samples SAMPLES File containing list of samples to include 246 Filtering options:
248 --region REGION Restrict to this region chrom:start-end 247 --samples SAMPLES File containing list of samples to include
249 248 --region REGION Restrict to this region chrom:start-end
250 Metrics to stratify results: 249
251 --stratify-fields STRATIFY_FIELDS 250 Metrics to stratify results:
252 Comma-separated list of FORMAT fields to stratify by 251 --stratify-fields STRATIFY_FIELDS
253 --stratify-binsizes STRATIFY_BINSIZES 252 Comma-separated list of FORMAT fields to stratify by
254 Comma-separated list of min:max:binsize to stratify each field on. Must be same length as --stratify-fields. 253 --stratify-binsizes STRATIFY_BINSIZES
255 --stratify-file STRATIFY_FILE 254 Comma-separated list of min:max:binsize to stratify each field on. Must be same length as
256 Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply stratification to 255 --stratify-fields.
257 both --vcf1 and --vcf2 256 --stratify-file STRATIFY_FILE
258 --period Report results overall and also stratified by repeat unit length (period) 257 Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply
259 258 stratification to both --vcf1 and --vcf2
260 Plotting options: 259 --period Report results overall and also stratified by repeat unit length (period)
261 --bubble-min BUBBLE_MIN 260
262 Minimum x/y axis value to display on bubble plots 261 Plotting options:
263 --bubble-max BUBBLE_MAX 262 --bubble-min BUBBLE_MIN
264 Maximum x/y axis value to display on bubble plots 263 Minimum x/y axis value to display on bubble plots
265 264 --bubble-max BUBBLE_MAX
266 Optional arguments: 265 Maximum x/y axis value to display on bubble plots
267 --verbose Print helpful debugging info 266
268 --numrecords NUMRECORDS 267 Optional arguments:
269 For debugging, only process this many records 268 --verbose Print helpful debugging info
270 --noplot Don't output any plots. Only produce text output 269 --numrecords NUMRECORDS
271 --vcftype1 VCFTYPE1 ##!!## Name trh could not be loaded 270 For debugging, only process this many records
272 --vcftype2 VCFTYPE2 ##!!## Name trh could not be loaded 271 --noplot Don't output any plots. Only produce text output
273 --ignore-phasing Treat all calls as if they are unphased 272 --vcftype1 VCFTYPE1 Name of genotyper that created the first vcf
274 273 --vcftype2 VCFTYPE2 Name of genotyper that created the second vcf
275 Version: 274 --ignore-phasing Treat all calls as if they are unphased
276 --version show program's version number and exit 275
276 Version:
277 --version show program's version number and exit
277 </help> 278 </help>
278 279
279 280
280 <citations> 281 <citations>
281 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats, 282 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,