Mercurial > repos > trinity_ctat > ctat_genome_resource_libs_data_manager_3
changeset 22:7b8726fb6a36 draft
retry...
| author | trinity_ctat |
|---|---|
| date | Sun, 21 Oct 2018 20:24:04 -0400 |
| parents | f403d561cda9 |
| children | 6bd663d53cb5 |
| files | data_manager/add_ctat_resource_lib.xml |
| diffstat | 1 files changed, 32 insertions(+), 13 deletions(-) [+] |
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--- a/data_manager/add_ctat_resource_lib.xml Fri Oct 19 18:01:53 2018 -0400 +++ b/data_manager/add_ctat_resource_lib.xml Sun Oct 21 20:24:04 2018 -0400 @@ -12,32 +12,48 @@ <![CDATA[ python $__tool_directory__/add_ctat_resource_lib.py --output_filename="${out_file}" - --display_name="${display_name}" - #if str($genome_resource_library.build_type) == "build_from_source": - --source_location "${genome_resource_library.source_location}" - #if str($genome_resource_library.rebuild) == "true": + --display_name="${display_name}" + #if str( $genome_resource_library.build_type ) == "download_and_build": + --download_url="${genome_resource_library.download_url}" + --download_location="${genome_resource_library.download_destination}" + #if str( $genome_resource_library.force_new_download ) == "true": + --new_archive_download + #end if + #if str( $genome_resource_library.keep_archive ) == "true": + --keep_archive + #end if + #if str( $genome_resource_library.rebuild ) == "true": --new_library_build #end if - if str($genome_resource_library.build_location) == "true": - --build_location="${genome_resource_library.different_build_location}" + if str( $genome_resource_library.specify_build_location.build_location ) == "different_location": + --build_location="${genome_resource_library.specify_build_location.different_build_location}" #end if - #end if - #if str($genome_resource_library.build_type) == "specify_built_location": + #elif str( $genome_resource_library.build_type ) == "build_from_source": + --source_location "${genome_resource_library.source_location}" + #if str( $genome_resource_library.rebuild ) == "true": + --new_library_build + #end if + if str( $genome_resource_library.specify_build_location.build_location ) == "true": + --build_location="${genome_resource_library.specify_build_location.different_build_location}" + #end if + #elif str( $genome_resource_library.build_type ) == "specify_built_location": --build_location="${genome_resource_library.built_library_location}" #end if - #if str($gmap_options.gmap_build) == "true": + + #if str( $gmap_options.gmap_build ) == "true": --gmap_build - #if str($gmap_options.force_gmap_build) == "true": + #if str( $gmap_options.force_gmap_build ) == "true": --force_gmap_build #end if #end if - #if str($mutation_lib_options.mutation_build) == "true": + + #if str( $mutation_lib_options.mutation_build ) == "true": --download_mutation_resources_url="${mutation_lib_options.source_url}" --cosmic_resources_location="${mutation_lib_options.cosmic_files_location}" - #if str($mutation_lib_options.force_download) == "true": + #if str( $mutation_lib_options.force_download ) == "true": --new_mutation_download #end if - #if str($mutation_lib_options.redo_integration) == "true": + #if str( $mutation_lib_options.redo_integration ) == "true": --new_mutation_integration #end if #end if @@ -105,6 +121,9 @@ <option value="same_as_download" selected="true">Build in Download location</option> <option value="different_location">Build in a different location</option> </param> + <when value="same_as_download"> + <!-- do nothing here --> + </when> <when value="different_location"> <param name="different_build_location" type="text" label="Build Location (full path)" /> </when>