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comparison qcSTR/qcSTR.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
139 </outputs> 139 </outputs>
140 140
141 141
142 <tests> 142 <tests>
143 <test> 143 <test>
144 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/> 144 <section name="required_arguments">
145 <param name="out" value="test"/> 145 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
146 <param name="vcftype" value="hipstr"/> 146 <param name="out" value="test"/>
147 </section>
148 <section name="optional_input_arguments">
149 <param name="vcftype" value="hipstr"/>
150 </section>
151
147 <output name="stdout" file="output.txt" /> 152 <output name="stdout" file="output.txt" />
148 <output_collection name="qcSTROutput" type="list" count="3"> 153 <output_collection name="qcSTROutput" type="list" count="3">
149 <element name="test-diffref-bias" ftype="pdf"> 154 <element name="test-diffref-bias" ftype="pdf">
150 <assert_contents> 155 <assert_contents>
151 <has_size value="12600" delta="300" /> 156 <has_size value="12600" delta="300" />
170 </output_collection> 175 </output_collection>
171 </test> 176 </test>
172 </tests> 177 </tests>
173 178
174 179
175 <help>usage: main.py [-h] --vcf VCF --out OUT [--vcftype {##!!## Name trh could not be loaded}] [--samples SAMPLES] [--period PERIOD] [--quality {per-locus,sample-stratified,per-sample,locus-stratified,per-call}] 180 <help>usage: pygalgen [-h] --vcf VCF --out OUT [--vcftype VCF_TYPE] [--samples SAMPLES]
176 [--quality-ignore-no-call] [--refbias-metric {mean,median}] [--refbias-mingts REFBIAS_MINGTS] [--refbias-xrange-min REFBIAS_XRANGE_MIN] [--refbias-xrange-max REFBIAS_XRANGE_MAX] 181 [--period PERIOD] [--quality {per-locus,sample-stratified,per-sample,locus-stratified,per-call}]
177 [--refbias-binsize REFBIAS_BINSIZE] [--numrecords NUMRECORDS] [--version] 182 [--quality-ignore-no-call] [--refbias-metric {mean,median}] [--refbias-mingts REFBIAS_MINGTS]
183 [--refbias-xrange-min REFBIAS_XRANGE_MIN] [--refbias-xrange-max REFBIAS_XRANGE_MAX]
184 [--refbias-binsize REFBIAS_BINSIZE] [--numrecords NUMRECORDS] [--version]
178 185
179 options: 186 options:
180 -h, --help show this help message and exit 187 -h, --help show this help message and exit
181 188
182 Required arguments: 189 Required arguments:
183 --vcf VCF VCF file to analyze. 190 --vcf VCF VCF file to analyze.
184 --out OUT Output prefix for files generated 191 --out OUT Output prefix for files generated
185 192
186 Optional input arguments: 193 Optional input arguments:
187 --vcftype {##!!## Name trh could not be loaded} 194 --vcftype VCF_TYPE Which type of VCF to restrict the input to, or 'auto' for no restrction
188 Which type of VCF to restrict the input to, or 'auto' for no restrction
189 --samples SAMPLES File containing list of samples to include 195 --samples SAMPLES File containing list of samples to include
190 --period PERIOD Only consider repeats with this motif length 196 --period PERIOD Only consider repeats with this motif length
191 197
192 Quality plot options: 198 Quality plot options:
193 --quality {per-locus,sample-stratified,per-sample,locus-stratified,per-call} 199 --quality QUALITY Which quality plot(s) to produce. May be specified more than once. See the README for more
194 Which quality plot(s) to produce. May be specified more than once. See the README for more info 200 info (per-locus,sample-stratified,per-sample,locus-stratified,per-call)
195 --quality-ignore-no-call 201 --quality-ignore-no-call
196 Exclude no-calls and calls without quality scores from quality graph distributions instead of the default, which is to include them as zero quality calls. Setting this can cause the plotting to crash if 202 Exclude no-calls and calls without quality scores from quality graph distributions instead of
197 it reduces the number of valid calls (in a strata) to &lt;= 1 203 the default, which is to include them as zero quality calls. Setting this can cause the
204 plotting to crash if it reduces the number of valid calls (in a strata) to &lt;= 1
198 205
199 Reference bias plot options: 206 Reference bias plot options:
200 --refbias-metric {mean,median} 207 --refbias-metric METRIC
201 Which metric to use for the y-axis on the reference bias plot. 208 Which metric to use for the y-axis on the reference bias plot. (mean,median)
202 --refbias-mingts REFBIAS_MINGTS 209 --refbias-mingts REFBIAS_MINGTS
203 Don't compute points for the reference bias plot based on fewer than this many genotypes 210 Don't compute points for the reference bias plot based on fewer than this many genotypes
204 --refbias-xrange-min REFBIAS_XRANGE_MIN 211 --refbias-xrange-min REFBIAS_XRANGE_MIN
205 Minimum x-axis value (bp) to show on the reference bias plot 212 Minimum x-axis value (bp) to show on the reference bias plot
206 --refbias-xrange-max REFBIAS_XRANGE_MAX 213 --refbias-xrange-max REFBIAS_XRANGE_MAX
211 Debug group: 218 Debug group:
212 --numrecords NUMRECORDS 219 --numrecords NUMRECORDS
213 Only process this many records 220 Only process this many records
214 221
215 Version: 222 Version:
216 --version show program's version number and exit 223 --version show program's version number and exit</help>
217 </help>
218 224
219 225
220 <citations> 226 <citations>
221 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats, 227 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
222 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek}, 228 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},