changeset 5:1abe9fb7c454 draft

planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9a42a858c5039edd1062e7a8a315c91c2c213000

--- a/data_manager/data_manager_select_index_by_path.xml	Fri Sep 08 10:56:11 2017 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Mon Sep 11 06:55:36 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/indexes.yml	Mon Sep 11 06:55:36 2017 -0400
@@ -0,0 +1,50 @@
+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
+gemini_databases:
+  name: gemini database
+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

--- a/data_manager/path_name_value_key_manager.py	Fri Sep 08 10:56:11 2017 -0400
+++ b/data_manager/path_name_value_key_manager.py	Mon Sep 11 06:55:36 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.json	Mon Sep 11 06:55:36 2017 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"fasta_indexes": [{"path": "test-data/sam_indexes/EboVir3.fa", "dbkey": "EboVir3", "name": "EboVir3", "value": "EboVir3"}]}}