# HG changeset patch
# User rhpvorderman
# Date 1505129631 14400
# Node ID 680110ffdcfe68de8ebea0eb12a489cf084533fc
# Parent  8ccfeedd1f037b2d0ab1d57a8d5c6452972795ce
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a

diff -r 8ccfeedd1f03 -r 680110ffdcfe data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Mon Sep 11 07:23:55 2017 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Mon Sep 11 07:33:51 2017 -0400
@@ -15,7 +15,7 @@
         <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." />
         <param name="path" type="text" value="" label="path field for the entry" />
         <param name="data_table" type="select" value="" label="data table for the index">
-          <option value='all_fasta --no_prefix'>all_fasta</option>
+          <option value='all_fasta'>all_fasta</option>
           <option value='bowtie2_indexes'>bowtie2_indexes</option>
           <option value='bowtie_indexes'>bowtie_indexes</option>
           <option value='bowtie_indexes_color'>bowtie_indexes_color</option>
@@ -25,7 +25,7 @@
           <option value='gatk_picard_indexes'>gatk_picard_indexes</option>
           <option value='gene_transfer'>gene_transfer</option>
           <option value='hisat2_indexes'>hisat2_indexes</option>
-          <option value='kallisto_indexes --no-prefix'>kallisto_indexes</option>
+          <option value='kallisto_indexes'>kallisto_indexes</option>
           <option value='picard_indexes'>picard_indexes</option>
           <option value='tophat2_indexes'>tophat2_indexes</option>
         </param>
diff -r 8ccfeedd1f03 -r 680110ffdcfe data_manager/indexes.yml
--- a/data_manager/indexes.yml	Mon Sep 11 07:23:55 2017 -0400
+++ b/data_manager/indexes.yml	Mon Sep 11 07:33:51 2017 -0400
@@ -2,6 +2,7 @@
   name: fasta file
   extensions:
     - .fa
+  no_prefix: True
 bowtie2_indexes:
   name: bowtie2 index
   extensions:
@@ -40,6 +41,7 @@
     - .ht2
 kallisto_indexes:
   name: kallisto index
+  no_prefix: True
 picard_indexes:
   name: picard index
 tophat2_indexes:
diff -r 8ccfeedd1f03 -r 680110ffdcfe data_manager/path_name_value_key_manager.py
--- a/data_manager/path_name_value_key_manager.py	Mon Sep 11 07:23:55 2017 -0400
+++ b/data_manager/path_name_value_key_manager.py	Mon Sep 11 07:33:51 2017 -0400
@@ -58,7 +58,6 @@
     parser.add_argument( '--path', action='store', type=str, default=None, help='path' )
     parser.add_argument( '--data_table_name', action='store', type=str, default=None, help='path' )
     parser.add_argument( '--json_output_file', action='store', type=str, default=None, help='path' )
-    parser.add_argument( '--no_prefix', action='store_true', help='Does not check the prefix but checks the path. Useful for indexes that reference a single file.')
     options = parser.parse_args()
 
     path = check_param("path", options.path)
@@ -75,7 +74,8 @@
     index_dict = indexes.get(data_table_name,{})
     index_name = index_dict.get('name','index')
     index_extensions = index_dict.get('extensions', [''])
-    if not options.no_prefix:
+    no_prefix = index_dict.get('no_prefix', False)
+    if not no_prefix:
         dirname = os.path.dirname(path)
         prefix = basename
         for extension in index_extensions:
diff -r 8ccfeedd1f03 -r 680110ffdcfe test.json
--- a/test.json	Mon Sep 11 07:23:55 2017 -0400
+++ b/test.json	Mon Sep 11 07:33:51 2017 -0400
@@ -1,1 +1,1 @@
-{"data_tables": {"fasta_indexes": [{"path": "test-data/sam_indexes/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}}
+{"data_tables": {"all_fasta": [{"path": "test-data/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}}