# HG changeset patch
# User jjohnson
# Date 1523916870 14400
# Node ID 8880c2e4b2ee2110409b0bffbdda4e838f84bfe6
# Parent  8ba71aead5bc4c411d41f58078c6c629d62cb25b
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty

diff -r 8ba71aead5bc -r 8880c2e4b2ee create_gffdb.py
--- a/create_gffdb.py	Sun Apr 08 13:26:47 2018 -0400
+++ b/create_gffdb.py	Mon Apr 16 18:14:30 2018 -0400
@@ -18,17 +18,37 @@
     parser.add_argument(
         'gff_sqlite',
         help="sqlite file")
+    parser.add_argument(
+        '--create_introns',
+        action='store_true',
+        help='')
+    parser.add_argument(
+        '--disable_infer_transcripts',
+        action='store_true',
+        help='')
+    parser.add_argument(
+        '--disable_infer_genes',
+        action='store_true',
+        help='')
+    parser.add_argument(
+        '-v', '--verbose', action='store_true', help='Verbose')
     args = parser.parse_args()
 
-    db = gffutils.create_db(args.input_gff, args.gff_sqlite)
+    db = gffutils.create_db(
+        args.input_gff, args.gff_sqlite,
+        disable_infer_transcripts=args.disable_infer_transcripts,
+        disable_infer_genes=args.disable_infer_genes)
     version = db.execute('SELECT version FROM meta').fetchone()[0]
-    print('version:%s' % version,file=sys.stdout)
+    print('version:%s' % version, file=sys.stdout)
     dialect = db.execute('SELECT dialect FROM meta').fetchone()[0]
+    if args.create_introns:
+        db.create_introns()
     info = json.loads(dialect)
     if 'fmt' in info:
-        print('format:%s' % info['fmt'],file=sys.stdout)
-    seqids = [r[0] for r in db.execute('SELECT distinct seqid  FROM features').fetchall()]
-    print('seqids:%s' % ','.join(seqids),file=sys.stdout)
+        print('format:%s' % info['fmt'], file=sys.stdout)
+    seqids = [r[0] for r in
+              db.execute('SELECT distinct seqid  FROM features').fetchall()]
+    print('seqids:%s' % ','.join(seqids), file=sys.stdout)
 
 
 if __name__ == "__main__":
diff -r 8ba71aead5bc -r 8880c2e4b2ee create_gffdb.xml
--- a/create_gffdb.xml	Sun Apr 08 13:26:47 2018 -0400
+++ b/create_gffdb.xml	Mon Apr 16 18:14:30 2018 -0400
@@ -1,13 +1,21 @@
-<tool id="create_gffdb" name="Create GFF DB for GTF or GFF3" version="0.1.0">
-    <description>gffutils sqlite db</description>
+<tool id="create_gffdb" name="Create gffutils SQLite DB" version="0.1.0">
+    <description>for GTF or GFF3</description>
     <requirements>
         <requirement type="package">gffutils</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        python '$__tool_directory__/create_gffdb.py' '$input' '$output'
+        python '$__tool_directory__/create_gffdb.py' $create_introns '$input' '$output'
     ]]></command>
     <inputs>
         <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/>
+        <param name="create_introns" type="boolean" truevalue="--create_introns" falsevalue="" checked="false" 
+             label="create intron features"/>
+        <param name="disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="true" 
+             label="disable_infer_transcripts (True for Ensmbl GTF)"
+             help="Can be more than 100 times slower if this is false"/>
+        <param name="disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="true" 
+             label="disable_infer_transcripts (True for Ensmbl GTF)"
+             help="Can be more than 100 times slower if this is false"/>
     </inputs>
     <outputs>
         <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" />
@@ -23,5 +31,7 @@
         </test>
     </tests>
     <help><![CDATA[
+Creates a SQLite database for a GTF or GFF3 feature file.   
+http://daler.github.io/gffutils/index.html
     ]]></help>
 </tool>