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comparison snpEff_create_db.xml @ 33:94653948fdb9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e4cbbb48006ac767c69efe53eab2a63306124bb5
author iuc
date Sat, 04 Oct 2025 17:00:46 +0000
parents ebe9fd7e5bd1
children
comparison
equal deleted inserted replaced
32:ebe9fd7e5bd1 33:94653948fdb9
124 </data> 124 </data>
125 </outputs> 125 </outputs>
126 <tests> 126 <tests>
127 <test expect_num_outputs="2"> 127 <test expect_num_outputs="2">
128 <param name="genome_version" value="pBR322"/> 128 <param name="genome_version" value="pBR322"/>
129 <param name="input_type_selector" value="gb"/> 129 <conditional name="input_type">
130 <param name="input" value="pBR322.gbk" /> 130 <param name="input_type_selector" value="gb"/>
131 <param name="input" value="pBR322.gbk" />
132 </conditional>
131 <output name="snpeff_output"> 133 <output name="snpeff_output">
132 <assert_contents> 134 <assert_contents>
133 <has_text text="pBR322" /> 135 <has_text text="pBR322" />
134 </assert_contents> 136 </assert_contents>
135 </output> 137 </output>
136 <output name="output_fasta" value="pBR322_test1.fna"/> 138 <output name="output_fasta" value="pBR322_test1.fna"/>
137 </test> 139 </test>
138 <test expect_num_outputs="2"> 140 <test expect_num_outputs="2">
139 <param name="genome_version" value="pBR322"/> 141 <param name="genome_version" value="pBR322"/>
140 <param name="input_type_selector" value="gb"/> 142 <conditional name="input_type">
141 <param name="input" value="pBR322.gbk.gz" /> 143 <param name="input_type_selector" value="gb"/>
144 <param name="input" value="pBR322.gbk.gz" />
145 </conditional>
142 <output name="snpeff_output"> 146 <output name="snpeff_output">
143 <assert_contents> 147 <assert_contents>
144 <has_text text="pBR322" /> 148 <has_text text="pBR322" />
145 </assert_contents> 149 </assert_contents>
146 </output> 150 </output>
147 <output name="output_fasta" value="pBR322_test1.fna"/> 151 <output name="output_fasta" value="pBR322_test1.fna"/>
148 </test> 152 </test>
149 <test expect_num_outputs="1"> 153 <test expect_num_outputs="1">
150 <param name="genome_version" value="pBR322"/> 154 <param name="genome_version" value="pBR322"/>
151 <param name="input_type_selector" value="gff"/> 155 <conditional name="input_type">
152 <param name="reference_source_selector" value="history"/> 156 <param name="input_type_selector" value="gff"/>
153 <param name="input_fasta" value="pBR322_test2.fna" /> 157 <param name="input" value="pBR322.gff3"/>
154 <param name="input" value="pBR322.gff3"/> 158 <conditional name="reference_source">
159 <param name="reference_source_selector" value="history"/>
160 <param name="input_fasta" value="pBR322_test2.fna" />
161 </conditional>
162 </conditional>
155 <output name="snpeff_output"> 163 <output name="snpeff_output">
156 <assert_contents> 164 <assert_contents>
157 <has_text text="pBR322" /> 165 <has_text text="pBR322" />
158 </assert_contents> 166 </assert_contents>
159 </output> 167 </output>
160 </test> 168 </test>
161 <test expect_num_outputs="1"> 169 <test expect_num_outputs="1">
162 <param name="genome_version" value="pBR322"/> 170 <param name="genome_version" value="pBR322"/>
163 <param name="input_type_selector" value="gff"/> 171 <conditional name="input_type">
164 <param name="reference_source_selector" value="history"/> 172 <param name="input_type_selector" value="gff"/>
165 <param name="input_fasta" value="pBR322_test2.fna.gz" /> 173 <param name="input" value="pBR322.gff3"/>
166 <param name="input" value="pBR322.gff3"/> 174 <conditional name="reference_source">
175 <param name="reference_source_selector" value="history"/>
176 <param name="input_fasta" value="pBR322_test2.fna.gz" />
177 </conditional>
178 </conditional>
167 <output name="snpeff_output"> 179 <output name="snpeff_output">
168 <assert_contents> 180 <assert_contents>
169 <has_text text="pBR322" /> 181 <has_text text="pBR322" />
170 </assert_contents> 182 </assert_contents>
171 </output> 183 </output>
172 </test> 184 </test>
173 <test expect_num_outputs="1"> 185 <test expect_num_outputs="1">
174 <param name="genome_version" value="Saccharomyces_mito"/> 186 <param name="genome_version" value="Saccharomyces_mito"/>
175 <param name="input_type_selector" value="gtf"/> 187 <conditional name="input_type">
176 <param name="reference_source_selector" value="history"/> 188 <param name="input_type_selector" value="gtf"/>
177 <param name="input_fasta" value="Saccharomyces_mito.fa.gz" /> 189 <param name="input" value="Saccharomyces_mito.gtf" />
178 <param name="input" value="Saccharomyces_mito.gtf" /> 190 <conditional name="reference_source">
191 <param name="reference_source_selector" value="history"/>
192 <param name="input_fasta" value="Saccharomyces_mito.fa.gz" />
193 </conditional>
194 </conditional>
179 <output name="snpeff_output"> 195 <output name="snpeff_output">
180 <assert_contents> 196 <assert_contents>
181 <has_text text="Saccharomyces_mito" /> 197 <has_text text="Saccharomyces_mito" />
182 </assert_contents> 198 </assert_contents>
183 </output> 199 </output>