Mercurial > repos > iuc > snpeff

comparison snpEff.xml @ 20:8f92c2b26e6d draft

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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
comparison
equal deleted inserted replaced
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">