Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference

changeset 5:f0c7cab2f547 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0
author sanbi-uwc
date Sat, 15 Sep 2018 03:20:01 -0400
parents 094bd0114876
children 6b54dcb42cd5
files data_manager/shapeit_ref.py data_manager/shapeit_ref.xml data_manager_conf.xml tool-data/shapeit_ref.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 13 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/shapeit_ref.py	Thu Sep 13 14:35:09 2018 -0400
+++ b/data_manager/shapeit_ref.py	Sat Sep 15 03:20:01 2018 -0400
@@ -37,6 +37,7 @@
     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')
+    parser.add_argument('sample_prefix', help='Filename prefix for sample file in this reference set')
     parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
     args = parser.parse_args()
 
@@ -45,15 +46,17 @@
 
     assert_prefix_exists(args.reference_prefix, args.path, 'reference')
     assert_prefix_exists(args.map_prefix, args.path, 'map')
+    assert_prefix_exists(args.sample_prefix, args.path, 'sample')
 
-    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'):
+    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix', 'sample_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, name=args.name, path=args.path,
-                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
+                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix,
+                            sample_prefix=args.sample_prefix)
     _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
 
     args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')
--- a/data_manager/shapeit_ref.xml	Thu Sep 13 14:35:09 2018 -0400
+++ b/data_manager/shapeit_ref.xml	Sat Sep 15 03:20:01 2018 -0400
@@ -1,11 +1,12 @@
-<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.5">
-    <command detect_errors="aggressive"><![CDATA[
+<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.6">
+    <command detect_errors="exit_code"><![CDATA[
     python $__tool_directory__/shapeit_ref.py
         '${value}'
         '${name}'
         '${path}'
         '${reference_prefix}'
         '${map_prefix}'
+        '${sample_prefix}'
         '${output_file}'
     ]]></command>>
     <inputs>
@@ -14,6 +15,7 @@
         <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" />
+        <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set">
     </inputs>
     <outputs>
         <data name="output_file" format="data_manager_json" />
--- a/data_manager_conf.xml	Thu Sep 13 14:35:09 2018 -0400
+++ b/data_manager_conf.xml	Sat Sep 15 03:20:01 2018 -0400
@@ -8,6 +8,7 @@
                 <column name="path" />
                 <column name="reference_prefix" />
                 <column name="map_prefix" />
+                <column name="sample_prefix" />
             </output>
         </data_table>
     </data_manager>    
--- a/tool-data/shapeit_ref.loc.sample	Thu Sep 13 14:35:09 2018 -0400
+++ b/tool-data/shapeit_ref.loc.sample	Sat Sep 15 03:20:01 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>
+#<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_  genetic_map_
+#1000G_Phase3	1000 Genomes project haplotypes		/path/to/shapeit_ref/1000G	1000GP_Phase3_chr	genetic_map_chr	1000GP_Phase3
--- a/tool_data_table_conf.xml.sample	Thu Sep 13 14:35:09 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Sat Sep 15 03:20:01 2018 -0400
@@ -1,6 +1,6 @@
 <tables>
     <table name="shapeit_ref" comment_char="#">
-        <columns>value, name, path, reference_prefix, map_prefix</columns>
+        <columns>value, name, path, reference_prefix, map_prefix, sample_prefix</columns>
         <file path="tool-data/shapeit_ref.loc" />
     </table>
 </tables>
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