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comparison deepvariant.xml @ 2:1071eaa424a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c
author iuc
date Sun, 04 Sep 2022 07:53:53 +0000
parents 97cc305f6afe
children 1a3c1f1a4d24
comparison
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1:97cc305f6afe 2:1071eaa424a2
132 <param name="region_literal" value="K03455:1-2669"/> 132 <param name="region_literal" value="K03455:1-2669"/>
133 </conditional> 133 </conditional>
134 <output name="vcf_file" ftype="vcf"> 134 <output name="vcf_file" ftype="vcf">
135 <assert_contents> 135 <assert_contents>
136 <has_text text="##fileformat=VCFv4.2"/> 136 <has_text text="##fileformat=VCFv4.2"/>
137 <has_size value="1846"/> 137 <has_size value="1842"/>
138 </assert_contents> 138 </assert_contents>
139 </output> 139 </output>
140 <output name="html_report" ftype="html"> 140 <output name="html_report" ftype="html">
141 <assert_contents> 141 <assert_contents>
142 <has_size value="18864" delta="100"/> 142 <has_size value="14880" delta="100"/>
143 </assert_contents> 143 </assert_contents>
144 </output> 144 </output>
145 </test> 145 </test>
146 <!-- Test region bed option--> 146 <!-- Test region bed option-->
147 <test expect_num_outputs="2"> 147 <test expect_num_outputs="2">
151 </conditional> 151 </conditional>
152 <param name="reads" value="reads.bam"/> 152 <param name="reads" value="reads.bam"/>
153 <param name="model_type" value="WGS"/> 153 <param name="model_type" value="WGS"/>
154 <conditional name="regions_conditional"> 154 <conditional name="regions_conditional">
155 <param name="regions_option" value="bed"/> 155 <param name="regions_option" value="bed"/>
156 <param name="bed_file" value="region.bed"/> 156 <param name="bed_file" value="region.bed" ftype="bed"/>
157 </conditional> 157 </conditional>
158 <output name="vcf_file" ftype="vcf"> 158 <output name="vcf_file" ftype="vcf">
159 <assert_contents> 159 <assert_contents>
160 <has_text text="##fileformat=VCFv4.2"/> 160 <has_text text="##fileformat=VCFv4.2"/>
161 <has_size value="1846"/> 161 <has_size value="1842"/>
162 </assert_contents> 162 </assert_contents>
163 </output> 163 </output>
164 <output name="html_report" ftype="html"> 164 <output name="html_report" ftype="html">
165 <assert_contents> 165 <assert_contents>
166 <has_size value="18864" delta="100"/> 166 <has_size value="14880" delta="100"/>
167 </assert_contents> 167 </assert_contents>
168 </output> 168 </output>
169 </test> 169 </test>
170 <!-- Test gvcf output option--> 170 <!-- Test gvcf output option-->
171 <test expect_num_outputs="3"> 171 <test expect_num_outputs="3">
181 <param name="region_literal" value="K03455:1-2669"/> 181 <param name="region_literal" value="K03455:1-2669"/>
182 </conditional> 182 </conditional>
183 <output name="vcf_file" ftype="vcf"> 183 <output name="vcf_file" ftype="vcf">
184 <assert_contents> 184 <assert_contents>
185 <has_text text="##fileformat=VCFv4.2"/> 185 <has_text text="##fileformat=VCFv4.2"/>
186 <has_size value="1846"/> 186 <has_size value="1842"/>
187 </assert_contents> 187 </assert_contents>
188 </output> 188 </output>
189 <output name="gvcf_file" file="output.g.vcf" ftype="vcf"> 189 <output name="gvcf_file" file="output.g.vcf" ftype="vcf">
190 <assert_contents> 190 <assert_contents>
191 <has_text text="##fileformat=VCFv4.2"/> 191 <has_text text="##fileformat=VCFv4.2"/>
192 <has_size value="3195"/> 192 <has_size value="3191"/>
193 </assert_contents> 193 </assert_contents>
194 </output> 194 </output>
195 <output name="html_report" ftype="html"> 195 <output name="html_report" ftype="html">
196 <assert_contents> 196 <assert_contents>
197 <has_size value="18864" delta="100"/> 197 <has_size value="14880" delta="100"/>
198 </assert_contents> 198 </assert_contents>
199 </output> 199 </output>
200 </test> 200 </test>
201 <!-- Test CRAM format input--> 201 <!-- Test CRAM format input-->
202 <test expect_num_outputs="2"> 202 <test expect_num_outputs="2">