Mercurial > repos > iuc > bcftools_gtcheck
comparison macros.xml @ 20:91c1e57d5c7f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8
author | iuc |
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date | Tue, 16 Jul 2024 17:05:16 +0000 |
parents | 3eac729e66c9 |
children | 7b4454382d39 |
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19:3eac729e66c9 | 20:91c1e57d5c7f |
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172 --fasta-ref '${section.fasta_ref}' | 172 --fasta-ref '${section.fasta_ref}' |
173 #end if | 173 #end if |
174 </token> | 174 </token> |
175 | 175 |
176 <xml name="macro_AF_file"> | 176 <xml name="macro_AF_file"> |
177 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> | 177 <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> |
178 </xml> | 178 </xml> |
179 <!-- This may need to bgzip and tabix the file --> | 179 <!-- This may need to bgzip and tabix the file --> |
180 <token name="@PREPARE_AF_FILE@"> | 180 <token name="@PREPARE_AF_FILE@"> |
181 <![CDATA[ | 181 <![CDATA[ |
182 #if 'AF_file' in $section and $section.AF_file: | 182 #if 'AF_file' in $section and $section.AF_file: |
189 --AF-file '${section.AF_file}' | 189 --AF-file '${section.AF_file}' |
190 #end if | 190 #end if |
191 </token> | 191 </token> |
192 | 192 |
193 <xml name="macro_estimate_AF"> | 193 <xml name="macro_estimate_AF"> |
194 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> | 194 <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> |
195 </xml> | 195 </xml> |
196 <token name="@ESTIMATE_AF@"> | 196 <token name="@ESTIMATE_AF@"> |
197 #if 'estimate_AF' in $section and $section.estimate_AF: | 197 #if 'estimate_AF' in $section and $section.estimate_AF: |
198 --estimate-AF "${section.estimate_AF}" | 198 --estimate-AF "${section.estimate_AF}" |
199 #end if | 199 #end if |