Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
diff data_manager_conf.xml @ 1:c5dea2080109 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Tue, 14 Aug 2018 11:19:49 -0400 |
| parents | 6cd60ba8a842 |
| children | 3888ec1918d0 |
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--- a/data_manager_conf.xml Tue Aug 14 11:14:52 2018 -0400 +++ b/data_manager_conf.xml Tue Aug 14 11:19:49 2018 -0400 @@ -1,32 +1,17 @@ <?xml version="1.0"?> <data_managers> -<data_manager tool_file="data_manager/data_manager_fetch_gff.xml" id="data_manager_fetch_gff"> - <data_table name="all_gff"> + <data_manager tool_file="data_manager/salmon_index_builder.xml" id="salmon_index_builder" version="0.1"> + <data_table name="salmon_indexes"> <output> <column name="value" /> <column name="dbkey" /> <column name="name" /> - <column name="path" output_ref="out_file"> - <move type="file"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gff/${path}</target> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gff/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - <data_table name="representative_gff"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" output_ref="out_file"> - <move type="file"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/representative_gff/${path}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/representative_gff/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>