Mercurial > repos > michal_klinka > trtools
comparison CompareSTR/compareSTR.xml @ 1:8e8cf43f6836 draft default tip
planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390
author | michal_klinka |
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date | Sun, 15 May 2022 15:23:59 +0000 |
parents | ecf8c4f9f8ba |
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0:ecf8c4f9f8ba | 1:8e8cf43f6836 |
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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, |