Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.18.1.2 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.18.1.1 |
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.18.1.0 |
gemini_annotate |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
gemini | 0.20.1 | package |
Additional information about this tool |
## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz #if $annotate_source.ext == 'vcf_bgzip': ## File is bgzipped and tabixed already -> just symlink data and index #set $tabixed_file = 'tabixed.vcf.gz' ln -s '$annotate_source' $tabixed_file && ln -s '$annotate_source.metadata.tabix_index' ${tabixed_file}.tbi && #else: ## bgzip and index vcf or bed #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext bgzip -c '$annotate_source' > '$tabixed_file' && tabix -p '$annotate_source.ext' '$tabixed_file' && #end if ## gemini annotate modifies its input database in-place so, in Galaxy, ## we need to create a copy first! cp '$infile' '$outfile' && gemini annotate -f '$tabixed_file' -a $a.a_selector #if $a.a_selector == 'extract': #set $types = [] #set $elements = [] #set $column_names = [] #set $operations = [] #for $action in $a.actions: $types.append(str($action.column_type)) $elements.append(str($action.element_to_extract).strip()) $column_names.append(str($action.column_name).strip()) $operations.append(str($action.operation)) #end for -t #echo ",".join($types) -e '#echo ",".join($elements)#' -o #echo ",".join($operations) -c '#echo ",".join($column_names)#' #else: -c '${a.column_name}' #end if #if str($annotate_source.ext) != "bed": $region_only #end if '$outfile'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
infile: gemini_load_result1.db annotate_source: anno.bed region_only: False a|column_name: anno5 a|a_selector: count |
name: value |
gemini_load_result1.db anno.bed value |
Test-2 |
infile: gemini_load_result1.db annotate_source: gemini_amend.vcf region_only: False a|column_name: anno5 a|a_selector: count |
name: value |
gemini_load_result1.db gemini_amend.vcf value |
Test-3 |
infile: gemini_load_result1.db annotate_source: gemini_amend.vcf.gz region_only: False a|column_name: anno5 a|a_selector: count |
name: value |
gemini_load_result1.db gemini_amend.vcf.gz value |
Test-4 |
infile: gemini_load_result1.db annotate_source: anno.bed a|actions_0|element_to_extract: 1 a|actions_0|column_name: anno5 a|actions_0|column_type: text a|actions_0|operation: first a|a_selector: extract |
gemini_load_result1.db anno.bed |
|
Test-5 |
infile: gemini_load_result1.db annotate_source: anno.bed a|actions_0|element_to_extract: 1 a|actions_0|column_name: anno5 a|actions_0|column_type: text a|actions_0|operation: first a|actions_1|element_to_extract: 2 a|actions_1|column_name: anno6 a|actions_1|column_type: integer a|actions_1|operation: first a|a_selector: extract |
gemini_load_result1.db anno.bed |