Mercurial > repos > iuc > data_manager_manual

changeset 4:1ed87dee9e68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit b775a4c6248f00430a9ab1b2a4e1afa255ac57a2"
author iuc
date Wed, 16 Oct 2019 05:16:25 -0400
parents 31f44a9f507e
children 744f607fac50
files data_manager/data_manager_manual.py data_manager/data_manager_manual.xml test-data/dbkeys.loc test-data/dm6.data_manager_json tool_data_table_conf.xml.test
diffstat 5 files changed, 47 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -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)
 
--- 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
@@ -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**
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dbkeys.loc	Wed Oct 16 05:16:25 2019 -0400
@@ -0,0 +1,2 @@
+#<dbkey>	<display_name>	<len_file_path>
+dm6	Drosophila melanogaster genome release 6	dm6.len
--- /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
@@ -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
--- /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
@@ -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>