# HG changeset patch
# User rhpvorderman
# Date 1505129035 14400
# Node ID 8ccfeedd1f037b2d0ab1d57a8d5c6452972795ce
# Parent  442b983d948e556347826c7b407a4ad67ce16aba
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d

diff -r 442b983d948e -r 8ccfeedd1f03 data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Mon Sep 11 07:22:49 2017 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Mon Sep 11 07:23:55 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.1">
+<tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2">
     <description>path inputer</description>
     <command interpreter="python">
         path_name_value_key_manager.py
@@ -14,8 +14,8 @@
         <param name="dbkey" type="text" value="" label="dbkey field for the entry.  Defaults to value if left blank." />
         <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="text" value="" label="data table for the index">
-          <option value='all_fasta'>all_fasta --no_prefix</option>
+        <param name="data_table" type="select" value="" label="data table for the index">
+          <option value='all_fasta --no_prefix'>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>
@@ -23,10 +23,9 @@
           <option value='bwameth_indexes'>bwameth_indexes</option>
           <option value='fasta_indexes'>fasta_indexes</option>
           <option value='gatk_picard_indexes'>gatk_picard_indexes</option>
-          <option value='gemini_databases'>gemini_databases</option>
           <option value='gene_transfer'>gene_transfer</option>
           <option value='hisat2_indexes'>hisat2_indexes</option>
-          <option value='kallisto_indexes'>kallisto_indexes --no-prefix</option>
+          <option value='kallisto_indexes --no-prefix'>kallisto_indexes</option>
           <option value='picard_indexes'>picard_indexes</option>
           <option value='tophat2_indexes'>tophat2_indexes</option>
         </param>
diff -r 442b983d948e -r 8ccfeedd1f03 data_manager/indexes.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/indexes.yml	Mon Sep 11 07:23:55 2017 -0400
@@ -0,0 +1,48 @@
+all_fasta:
+  name: fasta file
+  extensions:
+    - .fa
+bowtie2_indexes:
+  name: bowtie2 index
+  extensions:
+    - .bt2
+bowtie_indexes:
+  name: bowtie index
+  extensions:
+    - .ebwt
+bowtie_indexes_color:
+  name: bowtie color index
+  extensions:
+    - .ebwt
+bwa_mem_indexes:
+  name: bwa mem index
+  extensions:
+    - .amb
+    - .ann
+    - .bwt
+    - .pac
+    - .sa
+bwameth_indexes:
+  name: bwa_meth_index
+fasta_indexes:
+  name: fasta index
+  extensions:
+    - .fai
+gatk_picard_index:
+  name: picard index for GATK
+gene_transfer:
+  name: Gene Transfer File
+  extensions:
+    - .gtf
+hisat2_indexes:
+  name: hisat2 index
+  extensions:
+    - .ht2
+kallisto_indexes:
+  name: kallisto index
+picard_indexes:
+  name: picard index
+tophat2_indexes:
+  name: tophat2 index
+  extensions:
+    - .bt2
diff -r 442b983d948e -r 8ccfeedd1f03 data_manager/path_name_value_key_manager.py
--- a/data_manager/path_name_value_key_manager.py	Mon Sep 11 07:22:49 2017 -0400
+++ b/data_manager/path_name_value_key_manager.py	Mon Sep 11 07:23:55 2017 -0400
@@ -3,6 +3,7 @@
 import json
 import argparse
 import os
+import yaml
 
 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
@@ -32,6 +33,16 @@
     # Empty list should return False
     return bool(matched_files)
 
+def prefix_plus_extension_exists(directory, prefix, extension):
+    '''checks if files exist with prefix in a directory. Returns Boolean'''
+    matched_files = []
+    directory_files = os.listdir(directory)
+    for directory_file in directory_files:
+        if directory_file.startswith(prefix) and directory_file.endswith(extension):
+            matched_files.append(directory_file)
+    # Empty list should return False
+    return bool(matched_files)
+
 def main():
 
     #value = "test_value"
@@ -51,17 +62,6 @@
     options = parser.parse_args()
 
     path = check_param("path", options.path)
-
-    # Check if file or prefix exists
-    if not options.no_prefix:
-        dirname = os.path.dirname(path)
-        prefix = os.path.basename(path)
-        if not prefix_exists(dirname,prefix):
-            raise Exception( 'Unable to find files with prefix "{0}" in {1}.'.format( prefix, dirname ) )
-    else:
-        if not os.path.exists(path):
-            raise Exception( 'Unable to find path {0}.'.format( path ) )
-
     basename = os.path.basename(path)
     filename = os.path.splitext(basename)[0]
     name = check_param("name", options.name, default=filename)
@@ -70,6 +70,21 @@
     data_table_name = check_param("data_table_name", options.data_table_name)
     json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
 
+    # Check if file or prefix exists
+    indexes = yaml.load(file(os.path.join(os.path.dirname(__file__), 'indexes.yml')))
+    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:
+        dirname = os.path.dirname(path)
+        prefix = basename
+        for extension in index_extensions:
+            if not prefix_plus_extension_exists(dirname,prefix,extension):
+                raise Exception( 'Unable to find files with prefix "{0}" and extension "{1}" in {2}. Is this a valid {3}?'.format( prefix, extension, dirname, index_name ) )
+    else:
+        if not os.path.exists(path):
+            raise Exception( 'Unable to find path {0}.'.format( path ) )
+
     if os.path.exists(json_output_file):
         params = json.loads( open( json_output_file ).read() )
         print "params", params
diff -r 442b983d948e -r 8ccfeedd1f03 data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Sep 11 07:22:49 2017 -0400
+++ b/data_manager_conf.xml	Mon Sep 11 07:23:55 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/data_manager_select_index_by_path.xml" id="data_manager_select_index_by_path" version="0.0.1">
+    <data_manager tool_file="data_manager/data_manager_select_index_by_path.xml" id="data_manager_select_index_by_path" version="0.0.2">
         <data_table name="all_fasta">
             <output>
                 <column name="value" />
@@ -65,14 +65,6 @@
                 <column name="path" />
             </output>
         </data_table>
-        <data_table name="gemini_databases">
-            <output>
-                <column name="value" />
-                <column name="dbkey" />
-                <column name="name" />
-                <column name="path" />
-            </output>
-        </data_table>
         <data_table name="gene_transfer">
             <output>
                 <column name="value" />
diff -r 442b983d948e -r 8ccfeedd1f03 tool-data/gemini_databases.loc.sample
--- a/tool-data/gemini_databases.loc.sample	Mon Sep 11 07:22:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-## GEMINI databases
-#Version	dbkey	Description
-#08_08_2014	hg19	Database (08-08-2014)
diff -r 442b983d948e -r 8ccfeedd1f03 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Sep 11 07:22:49 2017 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Sep 11 07:23:55 2017 -0400
@@ -32,10 +32,6 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gatk_sorted_picard_index.loc" />
     </table>
-    <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/gemini_databases.loc" />
-    </table>
     <table name="gene_transfer" comment_char="#">
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/gene_transfer.loc" />