# HG changeset patch
# User sanbi-uwc
# Date 1536863709 14400
# Node ID 094bd011487614e3043bb0e3ad245cceccf8b945
# Parent  203133a920007988141281f72162b43747f1e5ea
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 06f9376308b504cd2ab7a4ff0126ae70d73faacc

diff -r 203133a92000 -r 094bd0114876 data_manager/shapeit_ref.py
--- a/data_manager/shapeit_ref.py	Thu Sep 13 10:03:16 2018 -0400
+++ b/data_manager/shapeit_ref.py	Thu Sep 13 14:35:09 2018 -0400
@@ -33,7 +33,7 @@
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
     parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
-    parser.add_argument('description', help='Description of reference set')
+    parser.add_argument('name', help='Description of reference set')
     parser.add_argument('path', help='Filesystem path to directory containing this reference set')
     parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
     parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
@@ -46,13 +46,13 @@
     assert_prefix_exists(args.reference_prefix, args.path, 'reference')
     assert_prefix_exists(args.map_prefix, args.path, 'map')
 
-    for column in ('key', 'description', 'path', 'reference_prefix', 'map_prefix'):
+    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'):
         value = getattr(args, column)
         if '\t' in value:
             exit("TAB character found in {} argument".format(column))
 
     data_manager_dict = {}
-    data_table_entry = dict(value=args.key, description=args.description, path=args.path,
+    data_table_entry = dict(value=args.key, name=args.name, path=args.path,
                             reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
     _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
 
diff -r 203133a92000 -r 094bd0114876 data_manager/shapeit_ref.xml
--- a/data_manager/shapeit_ref.xml	Thu Sep 13 10:03:16 2018 -0400
+++ b/data_manager/shapeit_ref.xml	Thu Sep 13 14:35:09 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.4">
+<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.5">
     <command detect_errors="aggressive"><![CDATA[
     python $__tool_directory__/shapeit_ref.py
         '${value}'
-        '${description}'
+        '${name}'
         '${path}'
         '${reference_prefix}'
         '${map_prefix}'
@@ -10,7 +10,7 @@
     ]]></command>>
     <inputs>
         <param name="value" type="text" label="Short key to identify this reference set (no spaces)" />
-        <param name="description" type="text" label="Description of the reference data" />
+        <param name="name" type="text" label="Description of the reference data" />
         <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
         <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" />
         <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
diff -r 203133a92000 -r 094bd0114876 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Sep 13 10:03:16 2018 -0400
+++ b/data_manager_conf.xml	Thu Sep 13 14:35:09 2018 -0400
@@ -4,7 +4,7 @@
         <data_table name="shapeit_ref">
             <output>
                 <column name="value" />
-                <column name="description" />
+                <column name="name" />
                 <column name="path" />
                 <column name="reference_prefix" />
                 <column name="map_prefix" />
diff -r 203133a92000 -r 094bd0114876 test-data/sample.out
--- a/test-data/sample.out	Thu Sep 13 10:03:16 2018 -0400
+++ b/test-data/sample.out	Thu Sep 13 14:35:09 2018 -0400
@@ -1,1 +1,1 @@
-{"data_tables": {"shapeit_ref": [{"description": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}}
+{"data_tables": {"shapeit_ref": [{"name": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}}
diff -r 203133a92000 -r 094bd0114876 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Sep 13 10:03:16 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Thu Sep 13 14:35:09 2018 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="shapeit_ref" comment_char="#">
-        <columns>value, description, path, reference_prefix, map_prefix</columns>
+        <columns>value, name, path, reference_prefix, map_prefix</columns>
         <file path="tool-data/shapeit_ref.loc" />
     </table>
 </tables>
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