| Previous changeset 3:31f44a9f507e (2019-10-16) Next changeset 5:744f607fac50 (2019-10-21) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit b775a4c6248f00430a9ab1b2a4e1afa255ac57a2" |
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modified:
data_manager/data_manager_manual.py data_manager/data_manager_manual.xml |
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added:
test-data/dbkeys.loc test-data/dm6.data_manager_json tool_data_table_conf.xml.test |
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| diff -r 31f44a9f507e -r 1ed87dee9e68 data_manager/data_manager_manual.py --- a/data_manager/data_manager_manual.py Wed Oct 16 03:19:50 2019 -0400 +++ b/data_manager/data_manager_manual.py Wed Oct 16 05:16:25 2019 -0400 |
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| @@ -168,8 +168,8 @@ data_table_entries = get_data_table_entries(params['param_dict'], options.galaxy_data_manager_data_path) # save info to json file - with open(filename, 'wb') as fh: - fh.write(json.dumps({"data_tables": data_table_entries})) + with open(filename, 'w') as fh: + fh.write(json.dumps({"data_tables": data_table_entries}, sort_keys=True)) get_file_content(params['param_dict'], target_directory) |
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| diff -r 31f44a9f507e -r 1ed87dee9e68 data_manager/data_manager_manual.xml --- a/data_manager/data_manager_manual.xml Wed Oct 16 03:19:50 2019 -0400 +++ b/data_manager/data_manager_manual.xml Wed Oct 16 05:16:25 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="data_manager_manual" name="Manual Data Manager" version="0.0.1" tool_type="manage_data"> +<tool id="data_manager_manual" name="Manual Data Manager" version="0.0.2" tool_type="manage_data" profile_version="19.01"> <options sanitize="False" /> <description>Entry Builder</description> <command detect_errors="exit_code"><![CDATA[ @@ -10,22 +10,22 @@ <repeat name="data_tables" title="Data Table to define" min="1"> <param name="data_table_name" type="select" multiple="False" optional="False" label="Choose Desired Data Table" dynamic_options="galaxy_code_get_available_data_tables( __trans__ )" refresh_on_change="True"/> - <repeat name="columns" title="Table Columns" min="1"> - <param name="data_table_column_name" type="select" multiple="False" optional="False" label="Column Name" - dynamic_options="galaxy_code_get_available_data_table_columns( __trans__, data_table_name )" /> - <!-- <param name="data_table_column_name" type="text" label="Column Name"/> --> - <param name="data_table_column_value" type="text" label="Value to use for data table column"/> - <conditional name="is_path"> - <param name="is_path_selector" type="select" label="Value is a path"> - <option value="yes">Yes</option> - <option value="no" selected="True">No</option> - </param> - <when value="yes"> - <param name="abspath" type="boolean" label="Apply abspath" checked="True" truevalue="abspath" falsevalue="" /> - </when> - <when value="no"/> - </conditional> - </repeat> + <repeat name="columns" title="Table Columns" min="1"> + <param name="data_table_column_name" type="select" multiple="False" optional="False" label="Column Name" + dynamic_options="galaxy_code_get_available_data_table_columns( __trans__, data_table_name )" /> + <!-- <param name="data_table_column_name" type="text" label="Column Name"/> --> + <param name="data_table_column_value" type="text" label="Value to use for data table column"/> + <conditional name="is_path"> + <param name="is_path_selector" type="select" label="Value is a path"> + <option value="yes">Yes</option> + <option value="no" selected="True">No</option> + </param> + <when value="yes"> + <param name="abspath" type="boolean" label="Apply abspath" checked="True" truevalue="abspath" falsevalue="" /> + </when> + <when value="no"/> + </conditional> + </repeat> </repeat> <repeat name="directory_content" title="Directory Content"> <param name="subdir" type="text" label="Place in Subdirectory" value=""/> @@ -58,6 +58,24 @@ <data name="out_file" format="data_manager_json" dbkey="dbkey"/> </outputs> <tests> + <test> + <repeat name="data_tables"> + <param name="data_table_name" value="__dbkeys__"/> + <repeat name="columns"> + <param name="data_table_column_name" value="value"/> + <param name="data_table_column_value" value="dm6"/> + </repeat> + <repeat name="columns"> + <param name="data_table_column_name" value="name"/> + <param name="data_table_column_value" value="Drosophila melanogaster genome release 6"/> + </repeat> + <repeat name="columns"> + <param name="data_table_column_name" value="len_path"/> + <param name="data_table_column_value" value="dm6.len"/> + </repeat> + </repeat> + <output name="out_file" file="dm6.data_manager_json"/> + </test> </tests> <help> **What it does** |
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| diff -r 31f44a9f507e -r 1ed87dee9e68 test-data/dbkeys.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dbkeys.loc Wed Oct 16 05:16:25 2019 -0400 |
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| @@ -0,0 +1,2 @@ +#<dbkey> <display_name> <len_file_path> +dm6 Drosophila melanogaster genome release 6 dm6.len |
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| diff -r 31f44a9f507e -r 1ed87dee9e68 test-data/dm6.data_manager_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dm6.data_manager_json Wed Oct 16 05:16:25 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"__dbkeys__": [{"len_path": "dm6.len", "name": "Drosophila melanogaster genome release 6", "value": "dm6"}]}} \ No newline at end of file |
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| diff -r 31f44a9f507e -r 1ed87dee9e68 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Oct 16 05:16:25 2019 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of dbkeys and len files under genome directory --> + <table name="__dbkeys__" comment_char="#"> + <columns>value, name, len_path</columns> + <file path="${__HERE__}/test-data/dbkeys.loc" /> + </table> +</tables> |