Mercurial > repos > iuc > data_manager_selection_background
changeset 2:e4f07770b340 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit f3390425582c26c4018eb13eb0f8f2a85189ce08"
| author | iuc |
|---|---|
| date | Tue, 24 Aug 2021 17:58:31 +0000 |
| parents | 0bd1cd5eac51 |
| children | 10ac95ec81d9 |
| files | data_manager/data_manager_selection_background.py data_manager/data_manager_selection_background.xml data_manager_conf.xml test-data/selection-out1.json tool-data/selection_background.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/data_manager/data_manager_selection_background.py Sat Aug 21 07:51:54 2021 +0000 +++ b/data_manager/data_manager_selection_background.py Tue Aug 24 17:58:31 2021 +0000 @@ -125,7 +125,7 @@ # Update Data Manager JSON and write to file data_manager_entry = { 'data_tables': { - 'bealign_selection': {'value': args.dbkey, 'label': args.label, 'path': table_entry} + 'selection_background': {'value': args.dbkey, 'label': args.label, 'path': table_entry} } }
--- a/data_manager/data_manager_selection_background.xml Sat Aug 21 07:51:54 2021 +0000 +++ b/data_manager/data_manager_selection_background.xml Tue Aug 24 17:58:31 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.1"> +<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.2"> <description>for selection analysis</description> <command detect_errors="exit_code"> <![CDATA[ @@ -38,7 +38,7 @@ <param name="label" value="SARS-CoV-2: ORF6" /> <param name="source_selector" value="history" /> <param name="dataset" value="selection-in1.fa" /> - <output name="out_file" file="selection-out1.json" /> + <output name="selection_background_json" file="selection-out1.json" /> </test> </tests> <help>
--- a/data_manager_conf.xml Sat Aug 21 07:51:54 2021 +0000 +++ b/data_manager_conf.xml Tue Aug 24 17:58:31 2021 +0000 @@ -5,12 +5,12 @@ <output> <column name="value" /> <column name="label" /> - <column name="path" output_ref="out_file" > + <column name="path" output_ref="selection_background_json" > <move type="file"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/selection/${path}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">selection_background/${value}/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/selection/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/selection_background/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/test-data/selection-out1.json Sat Aug 21 07:51:54 2021 +0000 +++ b/test-data/selection-out1.json Tue Aug 24 17:58:31 2021 +0000 @@ -1,1 +1,1 @@ -{"data_tables": {"bealign_selection": {"label": "SARS-CoV-2: ORF6", "path": "CoV2-ORF6.fa", "value": "CoV2-ORF6"}}} \ No newline at end of file +{"data_tables": {"selection_background": {"label": "SARS-CoV-2: ORF6", "path": "CoV2-ORF6.fa", "value": "CoV2-ORF6"}}} \ No newline at end of file
--- a/tool_data_table_conf.xml.sample Sat Aug 21 07:51:54 2021 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 24 17:58:31 2021 +0000 @@ -1,7 +1,7 @@ <tables> - <!-- Locations of dbkeys and len files under genome directory --> - <table name="bealign_selection" comment_char="#"> + <!-- Locations of background sequences for clade analysis --> + <table name="selection_background" comment_char="#"> <columns>value, label, path</columns> - <file path="tool-data/bealign_selection.loc" /> + <file path="tool-data/selection_background.loc" /> </table> </tables>