# HG changeset patch
# User sanbi-uwc
# Date 1537178684 14400
# Node ID 6b54dcb42cd519537e5ce19becd6540eb6fd9929
# Parent  f0c7cab2f5476ed042aaabba8cce018c6f846c1d
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9772b96ea77a4daac91b5fc87643972a1d71eda-dirty

diff -r f0c7cab2f547 -r 6b54dcb42cd5 data_manager/shapeit_ref.xml
--- a/data_manager/shapeit_ref.xml	Sat Sep 15 03:20:01 2018 -0400
+++ b/data_manager/shapeit_ref.xml	Mon Sep 17 06:04:44 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.6">
+<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.7">
     <command detect_errors="exit_code"><![CDATA[
     python $__tool_directory__/shapeit_ref.py
         '${value}'
@@ -31,4 +31,4 @@
     <citations>
         <citation type="doi">10.1038/nmeth.1785</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r f0c7cab2f547 -r 6b54dcb42cd5 test-data/sample.out
--- a/test-data/sample.out	Sat Sep 15 03:20:01 2018 -0400
+++ b/test-data/sample.out	Mon Sep 17 06:04:44 2018 -0400
@@ -1,1 +1,1 @@
-{"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_"}]}}
+{"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_chr", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_chr", "sample_prefix": "1000GP_Phase3"}]}}
diff -r f0c7cab2f547 -r 6b54dcb42cd5 tool-data/shapeit_ref.loc.sample
--- a/tool-data/shapeit_ref.loc.sample	Sat Sep 15 03:20:01 2018 -0400
+++ b/tool-data/shapeit_ref.loc.sample	Mon Sep 17 06:04:44 2018 -0400
@@ -1,7 +1,7 @@
 #This file lists the locations of SHAPEIT reference data connections
 #
-#<value>	<description>		<path>	<reference_file_prefix> <map_file_prefix>   <sample_file_prefix>
+#<value>	<description>	<path>	<reference_file_prefix>	<map_file_prefix>	<sample_file_prefix>
 #
 #For example
 #
-#1000G_Phase3	1000 Genomes project haplotypes		/path/to/shapeit_ref/1000G	1000GP_Phase3_chr	genetic_map_chr	1000GP_Phase3
+#1000G_Phase3	1000 Genomes project haplotypes	/path/to/shapeit_ref/1000G	1000GP_Phase3_chr	genetic_map_chr	1000GP_Phase3