Mercurial > repos > iuc > snpeff
comparison snpEff.xml @ 20:8f92c2b26e6d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
| author | iuc |
|---|---|
| date | Fri, 25 Jan 2019 12:29:48 -0500 |
| parents | 65ae79bddc69 |
| children | 5b80f544c67f |
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| 19:36dc3690a82c | 20:8f92c2b26e6d |
|---|---|
| 81 -dataDir '${snpDb.snpeff_db.extra_files_path}' | 81 -dataDir '${snpDb.snpeff_db.extra_files_path}' |
| 82 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' | 82 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}' |
| 83 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}' | 83 -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}' |
| 84 '${snpDb.snpeff_db.metadata.genome_version}' | 84 '${snpDb.snpeff_db.metadata.genome_version}' |
| 85 #else | 85 #else |
| 86 -dataDir "\$PWD/temp" | |
| 86 -download | 87 -download |
| 87 '$snpDb.genome_version' | 88 '$snpDb.genome_version' |
| 88 #end if | 89 #end if |
| 89 '$input' > '$snpeff_output' | 90 '$input' > '$snpeff_output' |
| 90 #if $statsFile: | 91 #if $statsFile: |
| 168 </options> | 169 </options> |
| 169 </param> | 170 </param> |
| 170 </section> | 171 </section> |
| 171 </when> | 172 </when> |
| 172 <when value="named"> | 173 <when value="named"> |
| 173 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> | 174 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> |
| 174 <help>@SNPEFF_DATABASE_URL@</help> | 175 <help>@SNPEFF_DATABASE_URL@</help> |
| 175 <validator type="empty_field" message="A genome version name is required" /> | 176 <validator type="empty_field" message="A genome version name is required" /> |
| 176 </param> | 177 </param> |
| 177 </when> | 178 </when> |
| 178 <when value="custom"> | 179 <when value="custom"> |