# HG changeset patch
# User sanbi-uwc
# Date 1466518322 14400
# Node ID 2b89ba1c0057bc7074eec4b629b5ff1769a01e0a
# Parent  db293ee25be543ab32122ef13fcfe188471889a9
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit c8c46a5600bb091d701b8cf78f80a50c6b6812f4

diff -r db293ee25be5 -r 2b89ba1c0057 data_manager/novocraft_index_builder.py
--- a/data_manager/novocraft_index_builder.py	Fri Apr 15 09:03:40 2016 -0400
+++ b/data_manager/novocraft_index_builder.py	Tue Jun 21 10:12:02 2016 -0400
@@ -4,7 +4,6 @@
 from __future__ import print_function
 import os
 import sys
-import urllib2
 import logging
 import argparse
 import shlex
@@ -16,13 +15,14 @@
 
 DEFAULT_DATA_TABLE_NAME = "novocraft_index"
 
-def get_dbkey_id_name(params, dbkey_description=None):
+def get_dbkey_id_name(params):
     # TODO: ensure sequence_id is unique and does not already appear in location file
     sequence_id = params['param_dict']['sequence_id']
     sequence_name = params['param_dict']['sequence_name']
-    if not sequence_name:
-        sequence_name = dbkey_description
-    return sequence_id, sequence_name
+    sequence_desc = params['param_dict']['sequence_desc']
+    if not sequence_desc:
+        sequence_desc = sequence_name
+    return sequence_id, sequence_name, sequence_desc
 
 def _make_novocraft_index(data_manager_dict, fasta_filename, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
     if os.path.exists(target_directory) and not os.path.isdir(target_directory):
@@ -50,25 +50,10 @@
     data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
     return data_manager_dict
 
-def download_from_url( data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
-    # TODO: we should automatically do decompression here
-    urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
-    fasta_reader = [urllib2.urlopen(url) for url in urls]
-
-    _make_novocraft_index(data_manager_dict, fasta_reader, target_directory, sequence_id, sequence_name, data_table_name)
-
-def download_from_history( data_manager_dict, params, target_directory,  sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
-    # TODO: allow multiple FASTA input files
-    input_filename = params['param_dict']['reference_source']['input_fasta']
-
-    _make_novocraft_index(data_manager_dict, input_filename, target_directory, sequence_id, sequence_name, data_table_name )
-
-REFERENCE_SOURCE_TO_DOWNLOAD = dict(url=download_from_url, history=download_from_history)
-
 def main():
     parser = argparse.ArgumentParser(description="Generate Novo-craft genome index and JSON describing this")
     parser.add_argument('output_filename')
-    parser.add_argument('--dbkey_description')
+    parser.add_argument('--input_filename')
     parser.add_argument('--data_table_name', default='novocraft_index')
     args = parser.parse_args()
 
@@ -79,12 +64,11 @@
     os.makedirs(target_directory)
     data_manager_dict = {}
 
-    sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description)
+    sequence_id, sequence_name, sequence_desc = get_dbkey_id_name(params)
 
-    # Fetch the FASTA
-    REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']]\
-        (data_manager_dict, params, target_directory, sequence_id, sequence_name, data_table_name=args.data_table_name or DEFAULT_DATA_TABLE_NAME )
+    #Make novocraft index
+    _make_novocraft_index(data_manager_dict, args.input_filename, target_directory, sequence_id, sequence_name, args.data_table_name or DEFAULT_DATA_TABLE_NAME )
 
     open(filename, 'wb').write(dumps( data_manager_dict ))
 
-if __name__ == "__main__": main()
+if __name__ == "__main__": main()
\ No newline at end of file
diff -r db293ee25be5 -r 2b89ba1c0057 data_manager/novocraft_index_builder.xml
--- a/data_manager/novocraft_index_builder.xml	Fri Apr 15 09:03:40 2016 -0400
+++ b/data_manager/novocraft_index_builder.xml	Tue Jun 21 10:12:02 2016 -0400
@@ -5,25 +5,21 @@
         <exit_code range=":-1" />
         <exit_code range="1:" />
     </stdio>
+    <requirements>
+        <requirement type="package" version="1.2">samtools</requirement>
+        <requirement type="package" version="3.04.01">novocraft</requirement>
+    </requirements>
     <command interpreter="python">
-        novocraft_index_builder.py "${out_file}" --data_table_name "novocraft_index"
+        novocraft_index_builder.py "${out_file}" --input_filename "${input_fasta.fields.path}" --data_table_name "novocraft_index"
     </command>
     <inputs>
         <param type="text" name="sequence_name" value="" label="Name of sequence" optional="False" />
         <param type="text" name="sequence_desc" value="" label="Description of sequence" />
         <param type="text" name="sequence_id" value="" label="ID for sequence" optional="False" />
-        <conditional name="reference_source">
-          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
-            <option value="url">URL</option>
-            <option value="history">History</option>
-          </param>
-          <when value="url">
-            <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" />
-          </when>
-          <when value="history">
-            <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" />
-          </when>
-        </conditional>
+        <param name="input_fasta" type="select" label="Genome to index(FASTA format)">
+            <options from_data_table="all_fasta"/>
+        </param>
+
     </inputs>
     <outputs>
         <data name="out_file" format="data_manager_json" />