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comparison deepvariant.xml @ 3:918c8b94c8d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
author iuc
date Mon, 10 Apr 2023 11:11:16 +0000
parents 98fe794d2ec0
children 63b68fe4af85
comparison
equal deleted inserted replaced
2:98fe794d2ec0 3:918c8b94c8d8
60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling"> 60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
61 <option value="WGS">WGS: Illumina whole genome sequencing</option> 61 <option value="WGS">WGS: Illumina whole genome sequencing</option>
62 <option value="WES">WES: Illumina whole exome sequencing</option> 62 <option value="WES">WES: Illumina whole exome sequencing</option>
63 <option value="PACBIO">PacBio HiFi</option> 63 <option value="PACBIO">PacBio HiFi</option>
64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option> 64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option>
65 <option value="ONT_R104">ONT R10.4 simplex and duplex data</option>
65 </param> 66 </param>
66 <conditional name="regions_conditional"> 67 <conditional name="regions_conditional">
67 <param name="regions_option" type="select" label="Select specific regions to process" help="Restrict the analysis to specific regions. A space-separated list of chromosome regions to process. Individual elements can be region literals, such as chr20:10-20 or paths to BED files."> 68 <param name="regions_option" type="select" label="Select specific regions to process" help="Restrict the analysis to specific regions. A space-separated list of chromosome regions to process. Individual elements can be region literals, such as chr20:10-20 or paths to BED files.">
68 <option value="disabled" selected="True">Disabled</option> 69 <option value="disabled" selected="True">Disabled</option>
69 <option value="region">Specify region literals</option> 70 <option value="region">Specify region literals</option>
108 <param name="regions_option" value="disabled"/> 109 <param name="regions_option" value="disabled"/>
109 </conditional> 110 </conditional>
110 <output name="vcf_file" file="output.vcf" ftype="vcf"> 111 <output name="vcf_file" file="output.vcf" ftype="vcf">
111 <assert_contents> 112 <assert_contents>
112 <has_text text="##fileformat=VCFv4.2"/> 113 <has_text text="##fileformat=VCFv4.2"/>
113 <has_size value="2473"/> 114 <has_size value="2478" delta="10"/>
114 </assert_contents> 115 </assert_contents>
115 </output> 116 </output>
116 <output name="html_report" file="report.html" ftype="html"> 117 <output name="html_report" file="report.html" ftype="html">
117 <assert_contents> 118 <assert_contents>
118 <has_size value="19287" delta="100"/> 119 <has_size value="23176" delta="100"/>
119 </assert_contents> 120 </assert_contents>
120 </output> 121 </output>
121 </test> 122 </test>
122 <!-- Test region literal option--> 123 <!-- Test region literal option-->
123 <test expect_num_outputs="2"> 124 <test expect_num_outputs="2">
132 <param name="region_literal" value="K03455:1-2669"/> 133 <param name="region_literal" value="K03455:1-2669"/>
133 </conditional> 134 </conditional>
134 <output name="vcf_file" ftype="vcf"> 135 <output name="vcf_file" ftype="vcf">
135 <assert_contents> 136 <assert_contents>
136 <has_text text="##fileformat=VCFv4.2"/> 137 <has_text text="##fileformat=VCFv4.2"/>
137 <has_size value="1842"/> 138 <has_size value="1843" delta="10"/>
138 </assert_contents> 139 </assert_contents>
139 </output> 140 </output>
140 <output name="html_report" ftype="html"> 141 <output name="html_report" ftype="html">
141 <assert_contents> 142 <assert_contents>
142 <has_size value="14880" delta="100"/> 143 <has_size value="18894" delta="100"/>
143 </assert_contents> 144 </assert_contents>
144 </output> 145 </output>
145 </test> 146 </test>
146 <!-- Test region bed option--> 147 <!-- Test region bed option-->
147 <test expect_num_outputs="2"> 148 <test expect_num_outputs="2">
156 <param name="bed_file" value="region.bed" ftype="bed"/> 157 <param name="bed_file" value="region.bed" ftype="bed"/>
157 </conditional> 158 </conditional>
158 <output name="vcf_file" ftype="vcf"> 159 <output name="vcf_file" ftype="vcf">
159 <assert_contents> 160 <assert_contents>
160 <has_text text="##fileformat=VCFv4.2"/> 161 <has_text text="##fileformat=VCFv4.2"/>
161 <has_size value="1842"/> 162 <has_size value="1843" delta="10"/>
162 </assert_contents> 163 </assert_contents>
163 </output> 164 </output>
164 <output name="html_report" ftype="html"> 165 <output name="html_report" ftype="html">
165 <assert_contents> 166 <assert_contents>
166 <has_size value="14880" delta="100"/> 167 <has_size value="18894" delta="100"/>
167 </assert_contents> 168 </assert_contents>
168 </output> 169 </output>
169 </test> 170 </test>
170 <!-- Test gvcf output option--> 171 <!-- Test gvcf output option-->
171 <test expect_num_outputs="3"> 172 <test expect_num_outputs="3">
181 <param name="region_literal" value="K03455:1-2669"/> 182 <param name="region_literal" value="K03455:1-2669"/>
182 </conditional> 183 </conditional>
183 <output name="vcf_file" ftype="vcf"> 184 <output name="vcf_file" ftype="vcf">
184 <assert_contents> 185 <assert_contents>
185 <has_text text="##fileformat=VCFv4.2"/> 186 <has_text text="##fileformat=VCFv4.2"/>
186 <has_size value="1842"/> 187 <has_size value="1843" delta="10"/>
187 </assert_contents> 188 </assert_contents>
188 </output> 189 </output>
189 <output name="gvcf_file" file="output.g.vcf" ftype="vcf"> 190 <output name="gvcf_file" file="output.g.vcf" ftype="vcf">
190 <assert_contents> 191 <assert_contents>
191 <has_text text="##fileformat=VCFv4.2"/> 192 <has_text text="##fileformat=VCFv4.2"/>
192 <has_size value="3191"/> 193 <has_size value="3192" delta="10" />
193 </assert_contents> 194 </assert_contents>
194 </output> 195 </output>
195 <output name="html_report" ftype="html"> 196 <output name="html_report" ftype="html">
196 <assert_contents> 197 <assert_contents>
197 <has_size value="14880" delta="100"/> 198 <has_size value="18894" delta="100"/>
198 </assert_contents> 199 </assert_contents>
199 </output> 200 </output>
200 </test> 201 </test>
201 <!-- Test CRAM format input--> 202 <!-- Test CRAM format input-->
202 <test expect_num_outputs="2"> 203 <test expect_num_outputs="2">
210 <param name="regions_option" value="disabled"/> 211 <param name="regions_option" value="disabled"/>
211 </conditional> 212 </conditional>
212 <output name="vcf_file" ftype="vcf"> 213 <output name="vcf_file" ftype="vcf">
213 <assert_contents> 214 <assert_contents>
214 <has_text text="##fileformat=VCFv4.2"/> 215 <has_text text="##fileformat=VCFv4.2"/>
215 <has_size value="2473"/> 216 <has_size value="2478"/>
216 </assert_contents> 217 </assert_contents>
217 </output> 218 </output>
218 <output name="html_report" ftype="html"> 219 <output name="html_report" ftype="html">
219 <assert_contents> 220 <assert_contents>
220 <has_size value="19287" delta="100"/> 221 <has_size value="23176" delta="100"/>
221 </assert_contents> 222 </assert_contents>
222 </output> 223 </output>
223 </test> 224 </test>
224 <!-- Test indexed reference format input--> 225 <!-- Test indexed reference format input-->
225 <test expect_num_outputs="2"> 226 <test expect_num_outputs="2">
233 <param name="regions_option" value="disabled"/> 234 <param name="regions_option" value="disabled"/>
234 </conditional> 235 </conditional>
235 <output name="vcf_file" ftype="vcf"> 236 <output name="vcf_file" ftype="vcf">
236 <assert_contents> 237 <assert_contents>
237 <has_text text="##fileformat=VCFv4.2"/> 238 <has_text text="##fileformat=VCFv4.2"/>
238 <has_size value="2473"/> 239 <has_size value="2478"/>
239 </assert_contents> 240 </assert_contents>
240 </output> 241 </output>
241 <output name="html_report" ftype="html"> 242 <output name="html_report" ftype="html">
242 <assert_contents> 243 <assert_contents>
243 <has_size value="19287" delta="100"/> 244 <has_size value="23176" delta="100"/>
244 </assert_contents> 245 </assert_contents>
245 </output> 246 </output>
246 </test> 247 </test>
247 </tests> 248 </tests>
248 <help><![CDATA[ 249 <help><![CDATA[