# HG changeset patch
# User sanbi-uwc
# Date 1536847396 14400
# Node ID 203133a920007988141281f72162b43747f1e5ea
# Parent  495439e68fca8745f52ae49fbafaf6a7f64cc090
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 74cb5dd2b3aaed4a5b26840b451b8f2920e4b9fe-dirty

diff -r 495439e68fca -r 203133a92000 data_manager/shapeit_ref.py
--- a/data_manager/shapeit_ref.py	Thu Sep 13 08:47:41 2018 -0400
+++ b/data_manager/shapeit_ref.py	Thu Sep 13 10:03:16 2018 -0400
@@ -52,7 +52,7 @@
             exit("TAB character found in {} argument".format(column))
 
     data_manager_dict = {}
-    data_table_entry = dict(key=args.key, description=args.description, path=args.path,
+    data_table_entry = dict(value=args.key, description=args.description, 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 495439e68fca -r 203133a92000 data_manager/shapeit_ref.xml
--- a/data_manager/shapeit_ref.xml	Thu Sep 13 08:47:41 2018 -0400
+++ b/data_manager/shapeit_ref.xml	Thu Sep 13 10:03:16 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.3">
+<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.4">
     <command detect_errors="aggressive"><![CDATA[
     python $__tool_directory__/shapeit_ref.py
-        '${key}'
+        '${value}'
         '${description}'
         '${path}'
         '${reference_prefix}'
@@ -9,7 +9,7 @@
         '${output_file}'
     ]]></command>>
     <inputs>
-        <param name="key" type="text" label="Short key to identify this reference set (no spaces)" />
+        <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="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" />
diff -r 495439e68fca -r 203133a92000 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Sep 13 08:47:41 2018 -0400
+++ b/data_manager_conf.xml	Thu Sep 13 10:03:16 2018 -0400
@@ -3,7 +3,7 @@
     <data_manager tool_file="data_manager/shapeit_ref.xml" id="data_manager_shapeit_reference">
         <data_table name="shapeit_ref">
             <output>
-                <column name="key" />
+                <column name="value" />
                 <column name="description" />
                 <column name="path" />
                 <column name="reference_prefix" />
diff -r 495439e68fca -r 203133a92000 test-data/sample.out
--- a/test-data/sample.out	Thu Sep 13 08:47:41 2018 -0400
+++ b/test-data/sample.out	Thu Sep 13 10:03:16 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)", "key": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}}
+{"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_"}]}}
diff -r 495439e68fca -r 203133a92000 tool-data/shapeit_ref.loc.sample
--- a/tool-data/shapeit_ref.loc.sample	Thu Sep 13 08:47:41 2018 -0400
+++ b/tool-data/shapeit_ref.loc.sample	Thu Sep 13 10:03:16 2018 -0400
@@ -1,6 +1,6 @@
 #This file lists the locations of SHAPEIT reference data connections
 #
-#<unique_key>	<description>		<path>	<reference_file_prefix> <map_file_prefix>
+#<value>	<description>		<path>	<reference_file_prefix> <map_file_prefix>
 #
 #For example
 #
diff -r 495439e68fca -r 203133a92000 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Sep 13 10:03:16 2018 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="shapeit_ref" comment_char="#">
+        <columns>value, description, path, reference_prefix, map_prefix</columns>
+        <file path="tool-data/shapeit_ref.loc" />
+    </table>
+</tables>
\ No newline at end of file
diff -r 495439e68fca -r 203133a92000 tool_data_tables_conf.xml.sample
--- a/tool_data_tables_conf.xml.sample	Thu Sep 13 08:47:41 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="shapeit_ref" comment_char="#">
-        <columns>key, description, path, reference_prefix, map_prefix</columns>
-        <file path="tool-data/shapeit_ref.loc" />
-    </table>
-</tables>
\ No newline at end of file